Aftermath
by johnliz4ever
Summary: It's been two months since Elizabeth was rescued from the Genii but the ordeal is not over yet. Sequel to What could have happened:The Eye. Rating as gone up to M for content in later chapters.
1. Chapter 1

**Aftermath.**

Disclaimer: I don't own Stargate Atlantis in any shape or form.

Note: I was never planning to write a sequel to "What could have happened: The Eye" but this just would not leave me alone. Anyway this is set one month after the end of "What could have happened: The Eye".

Pairings: John/Liz, mentions of Liz/Kolya.

Spoilers: Everything in season one.

**Atlantis **(One month later)

Elizabeth ran into the bathroom and shut the door. The sickness was getting worse. It had been on and off the last week and she felt terrible. She should go and see Carson. She'd been meaning too, but she was so busy trying to catch up on what she'd missed. She didn't have the time. She'd only been back two months.

Elizabeth sat on the floor with her back against the wall. She'd never felt so ill in her life. She really should see Carson, in case she brought back an infection from the Genii home world. She really didn't want the entire base stuck with this illness.

Elizabeth stood up, taking a moment to steady herself before putting the shower on and stepping under the warm spray. She let the water wash away all her worry, she ran her hands through her hair. She loved the morning. She could wake up and just for a minute just pretend that the Genii had never taken her. Although that didn't last, there would always be someone who, unintentionally, would say something that would remind her and then the whole base would spend the rest of the day tiptoeing around her so she wouldn't breakdown. She was sick of it.

Elizabeth stepped out of the shower and after she'd dried herself, her hair and got changed she made her way to the infirmary, trying to keep the sickness at bay long enough to actually get to Carson.

She walked into the infirmary and saw Carson talking to one of the nurses.

"Carson?"

Carson looked at Elizabeth and smiled. The nurse took that as her cue and left the two of them alone.

"Dr Weir, what can I do for you?"

Elizabeth walked over to Carson, she knew he was being cautious about what he was saying.

"I'm actually not feeling well. I keep being sick and dizzy."

Carson nodded to one of the beds and Elizabeth sat down.

"After what you've been through it's no wonder you're…"

Carson realised what he was saying and trailed off. This just pissed Elizabeth off more.

"Carson, you don't have to tiptoe around me, I'm not going to breakdown if someone mentions Kolya or the Genii."

Carson cleared his throat and looked at her apologetically.

"I'm sorry Elizabeth. We're all just so worried about you."

Elizabeth nodded.

"I know. I'm sorry I snapped at you."

The two friends smiled at each other and Carson began to examine her. He was about halfway through when something showed up that Carson didn't expect.

"Elizabeth, how long have you been feeling ill?"

Elizabeth shook her head trying to remember.

"About a week or so. Why?"

Carson couldn't meet her eyes instead he looked down at the notes he was making.

"Elizabeth, I'm going to need to take a blood test."

Elizabeth looked at him, confused at why Carson wouldn't meet her eyes.

"Carson, what's wrong with me"

Carson cleared his throat.

"I don't really want to say until I'm sure"

"Carson, please"

Carson looked into her eyes and saw her desperation. He ran a hand through his hair. He really didn't know how to tell her this.

"Elizabeth, please keep in mind that this is only a preliminary finding I could be completely wrong. Although the chances of me being wrong about this…"

"Carson"

Elizabeth interrupted him; Carson looked up at her.

"Elizabeth, you're eight weeks pregnant."

Elizabeth looked at the Scottish doctor in shock.

"No, no. I…I can't be pregnant."

Carson looked at her sympathetically.

"I'm sorry Elizabeth, but all the signs say you are…" Carson needed to know one thing, just one "…Elizabeth, please tell me it's Johns'"

John and Elizabeths' relationship was known throughout Atlantis, although nobody was actually sure when it when it began. Some were sure it started before the Genii attack some said after. The only two people who actually knew where John and Elizabeth.

"No."

Elizabeth croaked out and bust into tears. If John wasn't the father that only left one other person.

Kolya.

* * *

Elizabeth sat in shock on the infirmary bed as Carson drew some blood and began to analyse it. 

Elizabeth was trying to work through it all in her mind. She'd been back on Atlantis two months. She was two months pregnant. That must have meant she conceived the day or a few days before she was brought back to Atlantis. She placed her head in her hands.

Kolya was the only person she'd had sex with during the last seven months that would make her pregnancy possible. There had been a few times with John but that was no way close to the month she conceived in. Whether she liked it or not; she was pregnant and Kolya was the father.

Elizabeth wiped a tear from her eye. She didn't want this, she really didn't want this. Elizabeth had always loved children, but she never wanted to be a mother. It was one of the main things she and Simon had argued about. He wanted children but she was not ready to make that sort of commitment. Simon thought she was having an affair because of her lack of commitment to him. Simon always thought Elizabeth didn't want to commit herself fully to him. Maybe he was right. No doubt if Elizabeth had got pregnant while she was with Simon, she would have kept it. She couldn't get rid of a life she created but she also took precautions to prevent herself from getting pregnant. Of course, when she came to Atlantis she saw no reason to keep up with the precautions. Now she was wishing she did.

Carson walked over to her, results in his hands.

"Elizabeth, I was right. The blood tests confirmed it. You are pregnant."

Elizabeth sighed and Carson sat next to her lowering his voice.

"Elizabeth. Nobody has to find out about this. I can take care of it. If you want me too."

Elizabeths' head shot up. She couldn't believe Carson was asking her that. The man was viscously against abortion but he was setting aside his own Morals for her.

"Carson no."

Carson looked in her eyes.

"Elizabeth, if you don't want to go through with this pregnancy…"

"Carson no."

She repeated again.

Carson looked at her, she looked so small and fragile and Carson wanted to do anything to take that away even if it meant going against his own Moral code.

Carson took her hand in his.

"If that's what you want fine, but Elizabeth, what are you going to tell everyone? Especially John."

Elizabeth shook her head, tears falling from her eyes.

"I don't know."

Carson put his arm around Elizabeth and allowed her to cry on his shoulder as few tears fell from his own eyes.

TBC…


	2. Chapter 2

Disclaimer: I don't own Stargate Atlantis.

Elizabeths' crying had ceased and now Carson was holding her to offer comfort.

Elizabeth pulled herself from his hug and smiled at him.

"Thanks Carson."

Carson nodded and squeezed her hand.

"Anytime Love."

Elizabeth stood up and walked to the infirmary doors before turning back round to Carson.

"Carson, can you keep this between…"

Carson cut her off.

"No need to worry. I won't tell a soul."

Elizabeth gave him a smile of thanks before leaving. She walked through Atlantis to the balcony. She lent against it. Carson had given her something to stop the nausea, Morning Sickness; she corrected herself. She instinctively placed her hands on her abdomen. She knew she wouldn't be able to fell the baby yet. It was still a small embryo, which was slowly developing inside of her womb. She felt like she should hate it. She wanted to hate it, but she couldn't. Despite how it was conceived and who it's father was, it was still a part of her, it was still her child. It had done nothing wrong, How could she hate it?

The door to the balcony opened and John stepped out. He stood on the balcony next to her.

"Are you okay?"

She turned to face him and nodded. She didn't know how to tell him, she didn't know if she wanted to tell him yet. She quickly removed her hands from her abdomen; she didn't want him to find out that way. She wondered whether he'd hate her or resent the child. John ran a hand through her hair and down to her shoulders pulling her closer to him.

"Are you sure you're okay? You seem distant."

Elizabeth pulled herself out of his arms and took his hand.

"Come with me"

She pulled him off the balcony and led him to her quarters. She was contemplating what to tell him during the whole walk. Once they got to her quarters and she'd shut the door, John pulled her into his arms and tried to kiss her but she pulled back from him. John looked at her, the look on his face was somewhere between hurt and confusion.

"What's wrong?"

Elizabeth sat on her bed and gestured for John to join her. John took a seat next to her and grabbed her hand. She squeezed his hand and gave him a smile.

"John, I've got something to tell you."

John squeezed her hand back and gave her an encouraging smile.

"Whatever it is, you know you can tell me anything"

Elizabeth nodded

"I know"

Elizabeth released his hand, stood up and began to pace around the room.

"I went to see Carson earlier, he…um…he brought something to my attention"

She moved over to a small window on the east side off her room and looked out at the calming ocean. She was looked to look out onto the ocean. She loved to lose herself in its gentle waves. It calmed her. She needed that now.

John came up behind her and placed his hands on her shoulders. He turned her so she was facing him. He ran his hand down her cheek.

"What is it Elizabeth?"

Elizabeth looked everywhere except at him. She couldn't see the look on his face when she told him.

"John, I'm…I'm pregnant"

Elizabeth stood silent for a few moments, wondering if John had actually heard what she had said. She let her eyes gaze over at him and he was just stood there and she hoped he wasn't going to faint. She hadn't even told him the bulk of it, which was the fact the child was Kolya's and she was going to keep it.

John moved over to the bed, still in shock.

"You're…you're pregnant. Okay, I can handle this."

Elizabeth walked over to the bed and sat next to him.

"John that's not the only thing."

John shook his head,

"I don't think you could say anything that would shock me more at this moment."

Elizabeth shook her head.

"No, there really is"

She sat there for a few moments staring at her hands, as if they'd just becoming amazingly interesting, but she knew she was just putting off the inevitable.

"John…you're _not_ the father"

Elizabeth looked down at her hands again. She really didn't want to see the look on his face. She knew he must hate her at this moment. She felt John get off the bed and start pacing around the room.

"I don't mean to be rude or intrusive. But who the hell is?"

Tears formed in Elizabeths' eyes. John was hurt and she could hear it. He hated her and the child and she knew it. She might as wall tell him the rest, he couldn't hate her more then he already did. Elizabeth was shaking, was she scared to tell him? Was she worried her wouldn't understand?

"Kolya"

John continued to pace.

"What the hell as that bastard got to do with this?"

John stopped as soon as he said it and looked at her. No, no it couldn't be. She wouldn't have been as stupid as too have sex with the guy. But it wasn't her, it was who she was programmed to be. Johns' anger began to rise. She was having his child. She was pregnant with Kolya's child. There was a question leaning on Johns' mind, which he just had to ask.

"Are you keeping it?"

Elizabeth looked up at him sharply. He knew her well enough to know that the question was irrelevant.

"John, you know me well enough to know, I could never have an abortion."

John smiled, Elizabeth was confused, why the hell was he smiling?

John smiled turned into a laugh; Elizabeth knew what this laugh was.

"It's a joke isn't it…something you cooked up with Beckett…" John turned to her and looked deep in her eyes. His own eyes filling with tears "…Please tell me this some kind of sick joke"

Elizabeth sadly shook her head; John hit his hand against the wall making Elizabeth jump. She knew John was angry and upset but she'd never seen him like this. He was so insane with rage.

"And you're actually thinking about keeping _it_?"

Elizabeth answered her voice barely above a whisper.

"The baby has done nothing wrong John. I can't punish it. I'd never forgive myself."

John looked at her. His voice became calmer.

"Please Liz. Do you really think you'll be able to look at it everyday, knowing who it's father is?"

Elizabeth looked at the floor, the usually strong and confident Diplomat was unsure.

"It won't be easy but…"

John moved closer and cut her off, his voice building up with rage again.

"Don't you remember what he did to you? He tortured you. For God's sake Liz, he raped you."

Tears fell down Elizabeths' eyes.

"I know, I know"

She croaked out.

"But you still want it?"

Elizabeth nodded. John shook his head and stormed out of the room leaving Elizabeth. She sunk down onto the floor and began to cry. Unable to keep the tears at bay. She placed her hands on her abdomen again, wondering if John was right.

* * *

John stormed around the corridors just looking for somewhere, anywhere he could be alone with his thoughts. God, he wanted to hate her. Hate that child. He already hated Kolya. John walked into the Gym. It was empty. Thank God. Ford and Teyla were on the mainland with Markham. Bates, Stackhouse and the rest if their team where off world and Rodney didn't know where the gym was, so he wasn't there. John moved over to the punch bag and, after putting on the gloves, he began to beat the stuffing out of it. Quite literally, he punched it so hard in one part that he actually bust the bag. He didn't even notice. 

John stepped away from the bag and took off the gloves. His knuckles were bleeding but he didn't even notice the pain.

John heard someone enter the gym. He expected it to be Elizabeth, but was shocked when he discovered it was Carson, and Carson looked pissed.

"Dr Beckett, what can I do for you?"

Johns' voice was sharp and cold, he wasn't in the mood for this right now. Carson walked over to him.

"You really are a selfish prick do you know that?"

John stood in disbelief. This was a side of Carson he'd never seen before.

"What the hell is that supposed to mean?"

Carson stared at him, his eyes were filled with anger, but not hate.

"You really have no idea what she is going through do you? Elizabeth didn't ask for this, it was forced upon her…she needed your support, but you're so wrapped up in yourself that you didn't realise that."

Carson had found Elizabeth, only a few minutes earlier, crying in her room, practically begging him to terminate the pregnancy. When Carson asked her why she'd changed her mind she told him everything about what John had said. By the end of it, Carson was ready to put John in the infirmary. Carson told her to rethink the termination and forget about John said. Elizabeth promised him she would. After that Carson had gone in search off John, he didn't have to look very far, he knew where he would be. John had gone to the gym a lot when the Genii had taken Elizabeth and Rodney. He did it to get rid of his anger.

"Carson, you don't know anything about this. Its' none of your business."

Carson shook his head.

"I've just seen the state Elizabeth is in. She practically begged me for an abortion. Does that make you feel better? She's willing to get rid of her child for you. Is that what you want? If you really cared about Elizabeth at all, you'd let her make her own decisions and respect whatever decisions she makes."

Carson turned and left the gym before he punched John.

John turned back round to the punch bag, put the gloves on and started again, his vision obscured by the tears, which were falling out of his eyes.

TBC…

Carson may have been a little out of character, but I feel that if he'd just found Elizabeth the way she was, he'd be a little pissed at John, I was a little pissed at John.


	3. Chapter 3

Disclaimer: I don't own Stargate Atlantis, therefore I am making zero money out of this.

Note: Thanks to everyone who reviewed, it's good to know you didn't think Carson was OOC. Adding another pairing of Liz/Carson **Friendship.**

Carson walked through Atlantis. He shouldn't have done that. He was just so pissed at John. Carson knew it was difficult to hear that Elizabeth was pregnant with Kolya's child but she needed their support. Carson tried to rid himself of the look in her eyes. A look of pure desperation. She really needed Johns' support. She'd need everybody's support.

Carson ran his fingers through his hair. He'd be there for her, whenever she needed him. He was not going to desert her.

Carson walked into the infirmary, opened up a locked medicine cabinet and took something out. After locking, the cabinet back up he made his way through the corridors to Elizabeths' quarters. He knocked very gently on the door.

"Elizabeth, it's Carson"

He heard a very shaky 'come in'. Carson opened the door and found Elizabeth the way he'd left her, wrapped up in her bed, crying. The sound of her sobs forced Carson to think back to how he found her.

**Flashback**

Carson knocked on Elizabeths' door; he wanted to check she was okay. He was unsettled about something and he didn't know what.

There was no response to his first knock, so he tried again, this tome a little louder. When there was no response again. He guessed she was probably looking for John. He was about to walk away, when he heard a noise in Elizabeths' room. He was worried so he opened the door and stepped in. He saw her, huddled, on the floor with a protective hand on her abdomen. Carson, instantly, ran over to her small frame. He'd never seen such a strong woman like Elizabeth seem this fragile. He carefully wrapped her in his arms and let her cry. He assumed it was the hormones. They'd all have to get use to this. Elizabeth was muttering something to herself repeatedly.

Elizabeth looked at Carson; he eyes were still filled with tears before she lowered her head and muttered, as if in shame.

"Carson, I want the termination"

Carson looked at her in shock. Just under two hours ago, she'd scolded him for even mentioning it and now here she asking him for an abortion. Carson was shocked to say the least. He wanted to know what had happened to make her change her mind so quickly.

"Elizabeth, why the change of mind?"

Elizabeth looked at him, tears falling from her eyes as she tried furiously to rid herself of them.

"Does it matter? I just want this _thing_ out of me"

Carson gently ran his fingers through her hair. This wasn't Elizabeth Weir. This wasn't the woman he knew. Something had happened and he was going to find out what.

"Elizabeth, tell me what happened. I want to help."

His grip tightened around her and her head fell onto his shoulder as she told him everything.

She explained to him how she'd told John about the baby and how he reacted, how her told her she should get rid of the baby.

"I don't want him to feel I care for this baby more then him. I want him to be happy…"

Carson stopped listening; he knew what had happened. John had manipulated her, she was in a fragile state and he'd manipulated her. Elizabeth wouldn't want an abortion otherwise. Carson curled his fists into a ball. That selfish prick.

Carson looked down at Elizabeth again. He knew she didn't want a termination.

She knew she didn't want a termination.

Carson carefully released her from his arms and ran his hand down her cheek.

"Elizabeth, listen to me. Don't have an abortion just because he wants you to have one. You have to want one too. If you get rid of this baby, you will always regret it and you'll resent John."

Elizabeth nodded slowly listening to Carson. He wanted her to do the right thing. He wouldn't misguide her.

Carson unwrapped her from his arms and helped her onto the bed.

"I'll be back in a little while; I've got something to do. Think about what I said"

Elizabeth nodded and Carson left the room. Carson stood outside Elizabeths' room and placed his head in his hands cursing. How could John do that to her, if he really cared for her. Carson tried to calm himself down but there was only one way he would calm down. Telling John what he thought about him putting Elizabeth through all this.

**End of Flashback**

Carson snapped out his musing, walked over to Elizabeth, and sat next to her on the bed.

He ran his hand gently through her head. He wanted so much to be able to comfort her, but there was only so much he could do. Elizabeth sat up and smiled at Carson weakly and she brushed away her tears.

"You must think I'm a complete idiot"

Carson shook his head, he thought she was the strongest woman he'd ever met, to be able to put herself through that.

"Not at all"

He lightly wrapped one arm around her offering as much support as he could. He needed to know one thing though; what she was going to do about the baby.

"Have you decided what you're going to do, about the baby?"

Elizabeth nodded slightly.

"I'm going to keep it. You were right, I'd regret it if I got rid of it."

Carson nodded and took something out his pocket.

"Good, then I want you to take one of these vitamins everyday."

Elizabeth took the bottle and placed it on her nightstand. She gave him another smiled and wrapped him in a hug.

"Thank you Carson."

Carson hugged her back.

"You don't have to go though this alone"

He pulled back from the hug and after ordering her to get some rest he left the room and walked to the infirmary.

When he got there, he saw the one man he didn't want to see. John Sheppard.

He was sitting on the far bed having his hand bandaged up. Carson had noticed that Johns' hand had been bleeding earlier but at that point, he couldn't have cared less. John Sheppard had been a completely insensitive prick, but then again, it had to be hard on him as well. He wasn't thinking straight, he was upset.

Carson walked over to the nurse and finished bandaging Johns' hand.

"Are you going to talk to her?"

John looked up at Carson. John had managed to stop the tears but he was still hurting inside.

"Do you think it really will make a difference?"

Carson lowered his head slightly and answered John in a hushed tone.

"She's not getting rid of this baby, learn to accept that. But she'll need you, there's only so much I can do to help her. The support she needs will have to come from you."

John lowered his head.

"I can't, not knowing that…"

Carson cut him off by placing his hand on his shoulder.

"The baby has done nothing wrong John. It's Elizabeths' child, despite everything, she'll protect it, she'll care for it and she is going to love it, but will you be there to offer Elizabeth that support as well or will you desert her."

Carson walked away from John. John sat on the edge of the infirmary bed contemplating what Carson had just said. Would he be able to offer Elizabeth all the support she needed? John hung his head in shame. He couldn't.

TBC…


	4. Chapter 4

Disclaimer: I don't own Stargate Atlantis ****

Atlantis (2 Weeks later) 

Elizabeth didn't blame him, if she was honest with herself, she expected it. John might be strong but when it came to his emotions, he was weak, like a child. So when he told her a week ago that he couldn't be there for her through this, that he couldn't be strong for her, she accepted it. She didn't cry, didn't beg him to reconsider she just nodded, silently and he left.

Rumours were already flying around the city, somebody, probably Kavanagh, had found out she was pregnant and told everyone and while some knew that Kolya was the father, some mistakenly thought that John was the father and that he'd left her because he didn't want the baby. Whenever she heard anyone talking about it, she put them straight telling them that John wasn't the father and that Kolya was.

She wouldn't admit it but she missed John, how he used to be before the whole Genii incident. She missed his friendship, even though he'd promised her they could still be friends he'd been avoiding her for the past week.

Carson had been great. Helping her through everything, helping her with the pregnancy, helping her with John. She was grateful, but it wasn't the same.

Teyla had been trying so hard to help Elizabeth feel comfortable, even suggested she went to the Mainland for a break but Elizabeth had ensured her that she was fine.

So here she was, sat in her office finishing reports, trying to forget about all the people in the control room who were keeping a close eye on her. She was brought out of her trance by a knock on the door. She looked towards the glass and saw Rodney, she gestured for him to come in.

"What can I do for you Rodney?"

She knew exactly why he was here. It seemed like Teyla, Rodney, Ford, Peter and Carson were all taking it in turns to check-up on her every half-hour

Rodney began to babble incoherently about some aspect of the city.

"Rodney…stop it."

Rodney became quiet and looked at her.

"We're worried about you Elizabeth."

Elizabeth shook her head

"I'm not ill, I pregnant. Many women have gone though this before."

Rodney nodded and sat down opposite her. When Rodney had found out about her pregnancy his reaction had been similar to that of John. He couldn't believe she was even considering keeping the baby but after Carson talked with him he accepted the idea. He still had his doubts but he was going to help Elizabeth through this.

"Have you talked to…?"

"…John…" She finished off for him "…not recently"

She stopped typing and looked a Rodney. She knew he was expecting her to say something vindictive.

"What do you want me to say?"

Rodney shook his head and sat forward.

"I just thought you'd be a bit more emotional about it."

Elizabeth sighed and turned back to her laptop.

"John made a decision. I accept that. It's not his child."

Rodney closed his eyes. He wanted to tell her how much John still wanted to be with her, but he couldn't. Rodney wasn't usually good at keeping secrets but he'd promised John he wouldn't say a word. They were hurting each other so much though, maybe if they knew how the other felt they can try and put everything behind them.

"Elizabeth, you know I'm here for you, whenever you need a friend I'm…"

Elizabeth cut him off with a smile

"You're here, I know"

She gave him a warm smile, which he returned before leaving her office.

Rodney walked from Elizabeths' office into the control room, he saw John walking up the stairs.

"Major"

"Rodney"

Rodney saw Johns' gaze fall into Elizabeths' office, his eyes darkened with sadness before he turned back to Rodney.

"Why do you go see her?"

John looked at him confused.

"I've got nothing to talk to her about"

Rodney nodded knowingly. John had been doing this for the past week. He wouldn't talk to her, wouldn't be in the same room with her unless it was official but he'd come up to the control room and just stare at her.

"Why are you up here then?"

Rodney knew he'd lie.

"Oh, um, training it's cancelled; I've got something on the mainland to do"

Rodney nodded.

"Sure fine, it'll give me more time to work on this"

John nodded and after taking one last look at Elizabeth, he walked to the Jumper Bay.

Rodney sighed; John was still a mess.

**Flashback**

Rodney heard a knock at his door and reluctantly got out of bed, he was dying of flu and someone had the cheek to disturb him, typical he couldn't even die in peace. He opened the door and saw a very upset John behind it.

"Rodney, can I talk to you?"

Rodney let him in and shut the door. He knew John was having trouble accepting Elizabeths' pregnancy but he didn't expect John to get this upset.

John sat on the edge of Rodney's bed.

"I broke up with her; I've just left her when she needs me the most.

Rodney was not comfortable in these situations but he knew Ford was on assignment on the mainland so he was the only one left that John could talk to.

"She doesn't even hate me; I want her to hate me, she as the right to hate me."

Rodney knew John wasn't thinking right. Rodney sat down next to John. He tried to find the words to comfort John but he wasn't used to being the person people come to for support so he was making it as he went along.

"John…I know this is difficult for you, but…um…if it's what you want then it's for the best…"

John looked at him and cut him off.

"I still want to be with her but I can't…I can't accept that child"

Rodney understood, he was having trouble coming to terms with the revelation as well but Carson had managed to talk him round.

"John, despite the fact that it's father is a complete bastard, it's still Elizabeths' child as well. You would have to accept the child if you still want to be with Elizabeth"

John lowered his head and shook it. He didn't want any reminder of what Elizabeth went through, the child would remind him everyday.

Rodney hesitatively placed his hand on Johns' shoulder to offer support.

"Don't tell her what I've said, don't tell anyone"

Rodney nodded

"I won't say a word"

**End of Flashback**

Rodney gazed over to Elizabeth before continuing with his work. This whole thing was going to get worse before it got better.

**Mainland**

John was a mess, Elizabeth was a mess, the tension in the city was unbearable. Ford was glad to be out of there, even if it was just for one night. He felt sorry for John, he knew this was difficult for him, but it was so much harder for Elizabeth. John had took his shot and walked away, Elizabeth could never do that, she'd made a decision that was going to last for the rest of her life. Ford walked from the settlement when he saw the Jumper overhead. John embarked from the back of the Jumper looking a little worse-for-wear. Ford walked over to him

"Sir"

John nodded at him at walked over to the settlement. Ford knew his CO would eventually get over it but there would always be a reminder on Atlantis and he worried about how he would handle it. At the moment, he could pretend it didn't exists but all that would end on the day Elizabeth started to show.

TBC…


	5. Chapter 5

Disclaimer: I don't own Stargate Atlantis.

Note : I want to thank Patricia ( Dana-Carter) for Beta reading this chapter. Thanks for the reviews.

**Hazeydream**: Thank you. It's nice to know people think my fics are powerful and moving instead of freaky and weird. Anyway you are doing a great job with 'Two Turkey Sandwiches'

**MacCartney**: John is being an ass but it's all part of my master plan.

**Ashkash**Oh honey you've been with me for ages now, laugh at what you want. Anyway I understood what you were saying in your last review so don't worry. Anyway you're doing great with 'Stratagem' keep it up. :)**  
**

**TubaPrincess**You seem to have caught on to my plan. There's a reason this is happening and all will be explained in the next few chapters.

**Atlantis **(26 weeks later)

Elizabeth placed her hands on her abdomen. She was now about 8 months pregnant and things had slowly got back to semi normal. She and John could sit in a room together without everyone thinking they were going to breakdown. People had slowly got use to the fact she was pregnant. John among them. He slowly accepted the fact she was pregnant and although, obviously, he wasn't happy about it he had learnt to deal with it.

She leant her head back onto the infirmary pillows. Ford had brought her down here about an hour ago, despite her protests that she was fine, because the baby had been kicking like crazy and he was worried. She was really going to have to kick his ass. It was sweet that he was worried but everyone was acting like she was the only woman ever to be pregnant.

Elizabeth winced slightly as the baby kicked again. Elizabeth smiled. She'd really become attached to the baby and she hadn't even seen it yet but there was nothing like a bond between mother and child. She already loved it completely. She'd never loved anything so much before. Elizabeth never thought she'd settle into pregnancy and motherhood so well but she loved it. Despite the fact that everyone was fussing over her, that she hated.

Carson walked into the infirmary.

"How we now Elizabeth?"

Carson walked over to her, his heart was in the right place but she hated that he'd kept her in.

"_We_ want to get back to work"

Carson smiled and placed his hand on her abdomen. Out of everyone, Carson had been there for her the most. Carson smiled at he felt the baby kick.

"Wow, that's one strong boy"

Elizabeth looked at him sharply and he added.

"Or girl"

Elizabeth smiled at him.

* * *

John, who'd just heard from Ford about Elizabeth, walked into the infirmary unknown to Carson and Elizabeth. He stopped at the door and watched the moment pass between them. Needless to say the relationship between Carson and Elizabeth had hit the Atlantis rumour mills as more then friendship. John didn't believe any of the rumours, until now, until he saw the look pass between them. John walked away from the infirmary, a pang of jealousy filling his heart.

* * *

Carson finished examining Elizabeth. 

"Well the baby seems fine. Everything seems fine. Seems young Aiden was worried over nothing"

Elizabeth smiled at him.

"Thanks Carson"

Carson helped her from the bed.

"Anytime"

The two smiled at each other before Elizabeth left the infirmary.

* * *

John walked through the corridors of Atlantis trying to rid himself of the jealousy flowing through him. Sure, during the last 6 months she and Carson had become closer but he'd never bought into the rumours that there was something more going on between them. 

John stopped and lowered his head. Of course, something was going on between them. Carson had been there for Elizabeth where he had failed. Carson had got over the fact that the baby was Kolyas' so quickly and he was there for her when she needed him. It was obvious she'd start to feel something more for Carson.

John sighed, she'd moved on, she was over him. John knew it was a very self-centred think to think but…but some part of him still wanted her. A huge part of him still wanted her.

_Why couldn't he put everything aside and be with her? _

That was the question he could never put an answer to. Now it seems he wouldn't have to.

John was brought out of his musing when he felt a hand on his shoulder and his name being called.

"John"

John spun round and saw Elizabeth smiling nervously.

"Hi"

He smiled at her and pushed his hands into his pockets.

"I…uh…I heard you got took down to the infirmary earlier, are you okay? Are you both okay?"

Elizabeth smiled. John rarely asked how the baby was doing. It was nice that he finally asked.

"We're both doing fine. Aidens' chivalry as been kicked up a notch or two, he constantly worried about me"

Elizabeth mentally kicked herself as soon as she'd said it.

_Way to make John feel guilty Elizabeth._

John smiled at her.

"I've got to get back to work."

Elizabeth nodded.

"Me too. I'll see you around."

Elizabeth walked past John and he was about to head in the direction of the gym when he heard Elizabeth wince in pain. Without thinking he spun round to where she was standing against the wall with her hands on her abdomen.

"Are you okay?"

Elizabeths' eyes locked with his and she smiled at him.

"I'm fine; the baby is kicking like crazy"

John helped her off the wall and instinctively placed his arm around her waist.

"I'll take you to the infirmary"

Elizabeth shook her head.

"No, I'm fine. I'll just go to my quarters and rest.

John nodded and helped her to her quarters. She didn't protest to his hand which was round her waist and he didn't even seem to realise.

John helped her into her quarters and onto her bed. He drew the covers up over her and smiled. She looked so peaceful and sweet when she was like that.

"Can I get you anything? Water, magazine, chocolate?"

Elizabeth smiled at him.

"No thank you. I'm fine"

John smiled at her and brushed his hand against hers.

"I'll come and check on you later"

Elizabeth shook her head

"Really John, there's no need. I'm fine"

John nodded,

"I will come and check on you later"

John smirked at her before leaving her quarters. His smirked disappeared as soon as he was outside. He wanted her so much, wanted to be with her so much but he'd left it too late. She'd found someone else. John closed his eyes. Even if he couldn't be with her anymore he could still ensure that she was looked after properly, she and the baby.

John walked down the corridor in the direction of the infirmary.

* * *

John walked into the infirmary and saw Carson chatting with one of the nurses. John walked over to them. 

"Dr Beckett, can I have a word?"

Carson nodded and directed John into his office.

"What can I do for you Major?"

John didn't know how to start this conversation. He didn't want to sound like a jealous ex. Even though he was. He thought getting to the point would be his best course of action.

"Okay Carson. I know this is none of my business but just tell me one thing. You are going to look after Elizabeth and the baby aren't you?"

Carson was slightly confused but nodded none the less.

"Good, because if you make the same mistake I did or if you hurt her…lets just stay I won't stand for it."

John walked out of Carsons' office not even waiting for a response. Carson stood in stood in shock for a moment. John didn't think that…he and Elizabeth…? Good God, he'd better go set this thing straight.

Carson walked out of the infirmary and looked up and sown the corridors for John. He saw him walking down the corridor, which led to the gym.

"Major"

John turned round and saw Carson walking towards him.

"John, we need to talk"

Carson pulled him into a deserted corridor and looked at him.

"John, there is nothing going on between myself and Elizabeth"

Carson saw the look in Johns' eyes. He was not sure whether John believed him.

"I'm guessing you've heard a rumour about us but it's not true."

John shook his head.

"I saw the two of you. Earlier in the infirmary. You were both so…"

Carson put his hand on Johns' shoulder.

"I assure you John. Elizabeth and I are friends. That's all."

John looked down at the floor.

"I want her back"

John said it so quietly that Carson nearly didn't hear him. He raised his head and his eyes met with Carsons'.

"I want her back. God I'm so stupid. I want her back."

John smiled. It had taken something John thought was pretty drastic for him to realise it but John Sheppard wanted Elizabeth Weir back. He rushed past Carson and went to Elizabeths' quarters.

_God he'd missed her so much._

He knocked on the door and walked in. His smile fell as he saw Elizabeth wince in pain.

"Elizabeth"

He walked over to her and sat on the bed next to her.

"Honey, are you okay?"

Tears fell from Elizabeths' eyes as pain overtook her.

"No, I don't know what's wrong"

John thought for a moment. He really didn't want to move her but then again the infirmary might be the best place for her and it was close by.

John wrapped his arm around Elizabeth and helped her from the bed,

"Come on; let's get you to the infirmary"

Elizabeth moved slowly from the bed into Johns' arms as he helped steady her.

* * *

John and Elizabeth walked into the infirmary and John helped Elizabeth onto the nearest bed. 

"Carson, we need you"

Carson walked from his office over to Elizabeth.

"What's wrong?"

John glared at him.

"Call me crazy, but I think she's in labour."

Elizabeth looked at him in shock.

"No, it's not due for another 4 weeks"

Carson looked at her and shook his head.

"I'm afraid John might be right. That baby is coming and it'll be here soon."

John, who was sat next to Elizabeth on the bed holding her looked at him.

"How soon?"

Carson looked unsure

"I can't be sure until I find out how dilated she is but I'd say within the next few hours."

* * *

"Son of a bitch" 

Elizabeth cried as another contraction hit her. John was sat on the edge of the bed holding her hand. John had started to leave earlier but she'd begged him to stay, so he did.

John placed his arm around Elizabeths' shoulders. She dropped her head onto his arm.

"John, I don't think I want this baby."

John looked at her sharply.

"Elizabeth don't say that"

Elizabeth sighed and tears fell down her cheeks.

"I'm starting to think you were right"

John shook his head. Elizabeth couldn't start second guessing her decision now.

"You don't wanna listen to what I say."

Elizabeth continued to cry.

"What if I'm not a good mother? What if I can't look after it?"

John pulled her closer to him.

"You are going to be a fantastic mother and everyone is going to help you…especially me."

John let go of her hand and cupped her cheek. Tears threatening to fall from his own eyes.

"I'm going to be here for you and the baby. I promise you Lizzie"

John kissed the top of her head and held her. The hug was short lived as another contraction hit her.

"God damn it"

John smirked, never before had he heard Elizabeth swear so much and in so many different languages.

Carson walked over to them.

"Elizabeth I want you to push"

Elizabeth pushed and after she'd finished swearing in Russian and, John was fairly certain, Ancient, she heard a small cry. She leant her head onto the pillows behind her as Carson brought a small bundle towards them.

"You've got a daughter Elizabeth."

He placed the baby into her arms. Elizabeth looked at her baby; she saw Kolya. His twisted smile, the look in his eyes, the look of evil. She began to panic.

"Get it away from me. Carson take it."

Carson quickly took the baby away from her and John followed him.

"Carson, what's going on?"

Carson dragged John into his office. He still held the tiny bundle in his arms.

"I was afraid this might happen."

He ran a finger down the baby's cheek.

"Over the last few months Elizabeth as been conveniently letting herself forget who the father of this baby is. She can't hide from it anymore. It's not uncommon in rape victims who find themselves pregnant and keep the baby. It'll just take her a while to come round"

A nurse came to Carsons' office.

"Dr Beckett, Dr Weir is refusing to be checked over."

Carson nodded and looked around the infirmary for someone to take the baby.

"I'll take her"

John said walking over to Carson and taking the baby out of his arms. Carson looked at him in confusion.

"Are you sure?"

John looked down at the baby and nodded. He didn't even notice Carson leave the room. He was in awe. This baby was…perfect. She had beautiful emerald green eyes. Just like Elizabeth. She looked exactly like a mini-version of Elizabeth. Even though she couldn't see properly yet John felt like he beautiful eyes were just staring right at him.

John ran a finger down her cheek and one of her tiny hands grabbed it.

She was so innocent.

"Hi, you are just so adorable aren't you? You don't have to worry. Your mummy will be okay and I'm always going to be here for you. Remember that"

He gently kissed the baby's forehead.

* * *

Carson stood outside his office. He couldn't believe how, after months of resenting the baby, quickly John had become smitten by the baby. 

It was like John and Elizabeths' personalities had been reversed.

He wanted the baby, she didn't.

Carson sighed. It was going to be a long day.

TBC…


	6. Chapter 6

Disclaimer: I don't own Stargate Atlantis in any shape or form.

Note: Thanks to Patricia (Dana-Carter) for Beta reading.

**wolfdream**:You are doing a great job with 'Weathering the storm' and please do you original idea I'm dying to read it.**  
**

**Rhin Ariel**:Awww, you love my story. That is really sweet. Thanks for the positive feedback.

**Ashkash**: Somehow I knew you'd like how the feelings got reversed at the end. That's my favourite part. Plus I felt a little mean for everything I was putting John through because I really love him.

**Quezacolt**: Thanks. There are a few more chapters to this story but I've also got a sequel planned if the story works out well.

**TubaPrincess**: Thanks, glad you like the twist. The name of Elizabeths' daughter is going to be revealed soon, although not in this chapter. I've got to work through some things first but she will have a name soon.

**Hazeydream**: Thanks, I'm glad I made John an ass as well. It's just fun writing him when he's like that.

**Dark faith5: **Thanks, hope you enjoy Liz's reaction. It's coming up in this chapter.

* * *

Carson walked to Elizabeth. He felt sorry for the poor nurse who was trying to check her over. He walked over to the nurse and set her away. He sat in the chair next to Elizabeth. He was worried about her but knew he couldn't coddle her. 

"Are you going to stop being stubborn and let me check you over?"

Elizabeth looked at him sharply, the fear, which had entered her eyes a few moments before, was still there.

"I'm fine Carson"

Carson gently covered her hand with his.

"Elizabeth, please let me check you're okay"

Elizabeth closed her eyes and nodded. Carson breathed a sigh of relief, stood up and began to check her.

* * *

Rodney, Ford and Teyla walked into the infirmary. They'd just heard from one of the nurses that Elizabeth had just given birth and they wanted to check she was okay. As they walked through the doors they saw Elizabeth sitting on one of the nearest beds being check over by Carson. They were going to go over to her when Rodney stopped and stared into Carsons' office. It had to be a trick of the light. John Sheppard was in Carsons' office, holding gently a tiny bundle that was probably Elizabeths' baby. Ford and Teyla followed Rodney's gaze into the office. 

"That doesn't seem normal."

Ford commented and Rodney glared at him.

"Ya think!"

Rodney walked into Carsons' office. He could hear John whispering to the baby. His finger was still trapped in the grip of her tiny little hand.

Rodney walked up to him.

"Major, are you alright?"

John turned round and smiled at him.

"Yeah, yeah I'm fine. Rodney this is…well she doesn't have a name yet. Elizabeth hasn't exactly given her one yet but…isn't she just the sweetest little thing you've ever seen?"

Rodney looked at John confused. Was he drunk? For the last six months he'd wanted nothing to do with that baby and now he was…smitten.

"Yeah, she's beautiful. Are you sure you're okay?"

John sighed and looked at him.

"Rodney, for the last six months everyone as been telling me that this baby as done nothing wrong, that it's an innocent. I can finally see that. Why do you want to take that away from me?"

Johns' tone was almost accusive. Rodney put his hand on Johns' arm.

"I'm not trying to take anything away from you John. But why the change of heart?"

John looked down at the baby. Her little fists curled up in a ball. Her beautiful big eyes staring at him.

"Because she's just an innocent baby. She didn't ask for this life. It was given to her. She needs us. And at the minute, I don't think Elizabeth is very willing to be there for her."

Rodney looked at him in confusion.

"Why? What happened?"

John sighed, he hadn't meant to say that. Elizabeth didn't need psychobabble coming from Rodney's girlfriend and John knew Rodney would go and tell Kate.

"It's nothing, she's just a little…confused …at the moment. She'll be fine."

Rodney was genuinely concerned for the well-being of both Elizabeth and her daughter. He really did think that talking to Kate would be a good idea.

"Maybe she should talk to Kate…"

John immediately cut him off.

"Rodney no, Elizabeth doesn't need to talk to her. She'll come around in her own time."

Rodney shook his head.

"I don't know."

John looked out of Carsons' office window to where Elizabeth was sat on the bed.

"She'll be fine because she has too. It's her daughter."

Rodney nodded and left Carsons' office. He walked over to Teyla and Ford and dragged them out of the infirmary. Elizabeth needed some time alone.

* * *

John waited until the infirmary became quieter before going out to see Elizabeth. Rodney, Ford and Teyla had left over an hour ago and soon after that, many of the nurses had left. In the infirmary now there was, Beckett, a nurse, Elizabeth and of course John. Elizabeth had been sleeping for most of the hour and the baby had been getting checked over by Carson again. Apart from being a little premature, she was perfect. She was a beautiful healthy baby. She only had one problem. Her mother didn't want anything to do with her. 

John sighed and cradled the sleeping baby. She didn't even have a name yet. He didn't even know what Elizabeth wanted to call her. John closed his eyes. Maybe if he'd been there since the beginning Elizabeth wouldn't be like this.

"I'm so sorry sweetie. I should have been there for you and mummy since the beginning, then maybe this wouldn't have happened"

He looked over to where Elizabeth was sleeping; she began to stir. Maybe if John caught her in a good mood, she might accept the baby.

He left Carsons' office and began to walk over to Elizabeth. Carson stopped him.

"John, I don't think that's a good idea. Elizabeth is a mess right now. I don't think seeing the baby will help her much."

John shook his head. He understood Carsons' concern but he knew what he was doing.

"Carson. I need to do this. She needs to know that this baby is not a threat to her."

John walked around Carson, placed the baby in an Ancient version of a bassinet, and sat in the chair next to Elizabeths' bed. He was determined to make Elizabeth see sense. Elizabeth began to stir again. She opened one eye and smiled at John.

"Hi"

John smiled back, sat forward and held her hand.

"Hey, how are you feeling?"

Elizabeth sighed

"Tired, very tired"

Elizabeth began to sit up; she froze when she saw the baby in the bassinet.

"What the hell is that doing there?"

John sighed, let go of her hand and stood up. He went over to the bassinet and picked up the baby, who was now awake. John sat back down in his chair. Elizabeth stared at him.

"Elizabeth, this is your child. You wanted it"

Elizabeth shouted

"I didn't ask for that _that_"

John nodded.

"Yes, you are right. But she didn't ask for this life. But she got it and she got it because of you. Because you wanted to keep her. Call me crazy, but I think you even love her and that's what you're scared of. The fact that you love this child scares you because you know who the father is. She was conceived in a terrible way Elizabeth. But she's innocent."

Elizabeth looked away from him and he knew he was right. He just had to keep pushing her.

"When I first found out you were pregnant, I hated you and the baby so much. But neither of you had done anything wrong. Neither of you asked for what had happened, and that is what I've slowly been realising. You two are innocent parties in all this. But you both need each other. You've been thrown together, don't turn your back on her. On your daughter."

Elizabeth brushed away the tears, which had formed, in her eyes.

Was he right? Was everything he said true?

John slowly stood up, he walked the short distance between them and placed the baby in Elizabeths' arms. Elizabeth looked down at her. She was so small. She looked so much like Elizabeth and she couldn't understand how she'd seen Kolya in her before. Was it her mind playing tricks on her? It had too be. This baby was nothing like him.

* * *

Carson shook his head. He was bloody amazed as he saw Elizabeth run her finger down the cheek of her daughter. How the hell had John Sheppard managed to do that? 

Carson sighed. John wanted Elizabeth so badly. That much was obvious but for some reason he'd grown a strong attachment to the baby as well in such a short period of time. Maybe for once something was going right for them. Then again, don't speak too soon.

TBC…


	7. Chapter 7

Disclaimer: I don't own Stargate Atlantis.

Note: I blame the name of the baby on my current obsession with 'Desperate Housewives' and a certain singer. This is unbeta'd so any mistakes are my own.

**Hazeydream: **Thanks, it may get easier for them; it may not. I'm not giving anything away. You'll find out in this chapter.

**TubaPrincess: **Glad you liked the last chapter.

**MacCartney: **Thanks, I actually visualized John holding the baby when I wrote that part.

_

* * *

He pushed her hard against the wall and placed his lips onto hers.  
His hands roaming underneath her shirt finally succeeding in removing it.  
She kissed him back hungrily, wanting him as much as he wanted her.  
His lips moved down her neck. Biting, sucking, kissing every part of her. He pushed her into the wall harder. Her legs slipping around his waist.  
Her hands were busily removing his belt and unzipping his trousers.  
She moaned with pleasure as his mouth left her neck and moved down to her breast.  
When he heard the moan, he pulled her off the wall and pushed her onto their bed.  
She moved her hand behind his head and pushed him down to kiss her.  
He moved from her lips and looked into her passion filled eyes._  
"_I love you Elizabeth"_

_She smiled and kissed him passionately _

"_I love you Acastus"_

* * *

Elizabeth woke up sweating, shaking, terrified. She'd been having that dream regularly since her daughter, Bree she finally named her, was born. Elizabeth knew it was more then a dream, it was more than a nightmare, it was a memory and she was fairly certain it was the memory of the night Bree was conceived. The night before she was rescued .Elizabeth hadn't told anyone not even John. An arm protectively wrapped itself around her waist. She looked down at John. He was sleeping, so peacefully. It was calming to watch and she was glad she had that back. She heard a whimper in the room connected to theirs. She carefully and silently left Johns' grip and walked over to the connecting room. As she entered, the whimpering stopped and babbling started. 

Elizabeth walked over to the cradle and gently picked up her daughter. Since Johns' little speech four months ago, Elizabeth had slowly become closer to her daughter again.

"Hey, why are you awake? It's way past your bedtime"

The baby just gurgled at her and Elizabeth smiled. She really was the sweetest little baby Elizabeth had ever seen.

"Go back to sleep Bree."

Elizabeth cradled her in her daughter in her arms and gently shushed her.

Two arms wrapped themselves around her waist while a kiss was placed on her neck. John placed his head in the crook of her neck.

"Is she okay?"

Elizabeth nodded and the arms grew tighter around her waist.

"Yeah, she just wanted some attention"

Elizabeth drew a finger down her daughters' hand, which Bree grabbed on to.

Elizabeth didn't know why she'd called her daughter Bree. The name stuck in her memory for some reason.

John moved away from Elizabeth, breaking Elizabeth from her musing, and took Bree out of her arms. He kissed the top of her head and placed her back in her cradle.

"Sweet dreams Bree"

Elizabeth looked inside the cradle and saw Bree sleeping peacefully. She smiled and followed John back into their room, forgetting about her nightmare.

**

* * *

Atlantis **(A few hours later)

Elizabeth slowly opened her eyes. The sunlight was shining softly through the window of their room. She closed her eyes to the light. She was so tired. She'd woken up twice during the night again with that same memory of her and Kolya.

Elizabeth turned her back to the window and snuggled her head into her pillow. If she could just stay here, everything would be perfect. Elizabeth didn't even realise when someone came into the room and sat next to her on the bed.

Elizabeth felt something on her back and reluctantly turned around. She opened her eyes and saw John sat next to her with Bree in his arms and Bree was currently hitting her because of her involuntary arm movements.

Elizabeth slowly sat up and took Bree out of Johns' arms.

"Good morning honey. And John"

John lent in and kissed her.

"Good morning to you too."

Elizabeth tried to suppress a yawn but John caught her. He took Bree out of her arms and placed her on the bed, propping her up with pillows so she wouldn't fall.

"Have you been sleeping properly?"

He was concerned, bless him, but still it was very annoying that she couldn't even yawn anymore without people worrying.

"I'm fine…mum"

John smirked

"Cute, very cute"

He lent in to kiss her again only to be distracted by babbling coming from next to them. She looked and saw Bree thrashing her hands about obviously looking for attention. He gently kissed Elizabeth and Bree's babbling became a cry.

"Knew it"

He picked Bree up and kissed her forehead.

"You just want attention don't you?"

John smiled, sat next to Elizabeth and pulled Bree onto his chest.

"You just love attention don't you? She must get that from you Elizabeth"

John instantly froze. He didn't mean that. Everyone knew better then to say things like that, because it only made them think about the things she got from Kolya.

"I'm sorry Elizabeth, I didn't mean…"

Elizabeth cut him off and nodded

"It's okay…I'm going to get a shower"

Elizabeth quickly left the bed, got her things and went into the bathroom.

John sighed

"Damn it"

He looked down at Bree who was sat quietly like she knew what happened.

"I'm sorry baby. I didn't mean to remind her of…well you know who"

He kissed her forehead.

"Forgive me?"

Bree smiled and began to babble again.

John smiled. Who'd have guessed that he'd become so attached to Bree in such a short amount of time. He loved her completely. Like she was his. Except she wasn't, she wasn't his child. He didn't have anything to do with Bree despite the fact that he was sleeping with her mother. She was not his family, but she felt like it. He'd do anything to keep her safe. John kissed the top of her head. He'd do anything for her.

_

* * *

Elizabeth dropped her head in her hands. She'd had a hell of a day. First she'd had been avoiding John since he made that comment. She couldn't blame him, it just slipped out but she was still uncomfortable with it. _

_Then John had to go to the mainland, on his day off, which meant she had too look after Bree on which turned out to be her busiest day ever. Half-way through the day she went to the infirmary and practically begged Carson too look after Bree so she could have her briefings in peace. He agreed, he loved looking after Bree and he didn't have a busy day. _

_She sighed as someone knocked on the door. _

"_Come in"_

_She didn't even bother to remove her head from her hands. All she wanted to do was go down to her quarters; curl up in Johns' arms and go to sleep. The door to her quarters opened and someone walked into the room. She heard the sweet babbling of her beautiful baby girl. Elizabeth lifted her head from her hands and froze. No he couldn't be here. How would he have got here? Kolya was sat across from her holding Bree._

"_She'll always be my child, despite what you tell her. She'll always be a part of me Elizabeth. She'll always be a symbol of our love"_

"_Elizabeth…Elizabeth…Lizzie"_

* * *

"Lizzie" 

Elizabeth head shot up from her hands

"Kolya"

She looked at the John. His face showed clearly his confusion.

"Are you going tell me what you're dreaming about Elizabeth?"

Elizabeth rubbed her hands across her face trying to rid herself of the memory.

"Bree?"

John shook his head. He was confused

"She's with Carson, Peter just told me. I've just got back from the mainland. Are you going to tell me what happened?"

John was talking so fast, Elizabeth had missed half of what he said. She didn't know whether she'd be able to explain to him. Whether he'd understand.

"I've been dreaming a lot…of Kolya. Of him taking Bree…I've been waking up from memory in the form of nightmares. Things that actually happened when I was with the Genii."

John shook his head. He was concerned for her but she had nothing to worry about.

"Elizabeth, Kolya is not coming after you or Bree, he's is dead. I made damn sure of that"

Elizabeth shook her head and dropped it in shame.

"He's not dead"

John thought he heard wrong, she was talking quietly

"Please tell me you didn't just say Kolya is alive?"

Tears fell from Elizabeths' eyes and rage threatened to slowly engulf John. John closed his eyes briefly. He didn't want to become angry at Elizabeth. She might not even be right.

Slowly John opened his eyes and looked at Elizabeth.

"How can you be sure he's alive?"

It was Elizabeths' turn to close her eyes. She thought back to the Genii Home world, when she ran to Kolya, checked his pulse.

"His pulse was weak, it was there, but it was very weak. I thought he would die before Cowen and the backups got there. That's why I told you he was dead. But now, I'm not too sure. Kolya was strong, he'd been shot before and he lived, why would this time be any different?"

Elizabeth thought back to the time when she was Elizabeth Kolya. When Acastus had been shot while on a mission. She looked after him, they didn't think he would make it but he did. It was entirely possible he'd lived again. It wouldn't surprise her.

"How can you be sure though? I hit him pretty damn close to his heart"

Elizabeth shook her head.

"Not close enough to kill him instantly. You were about 2 centimetres from the bottom of his heart. Kolya is alive I know it"

John walked around to Elizabeth and held her hands.

"Don't worry. He doesn't know about Bree. She's safe. The Genii will not attack us again. You have my word."

John pulled Elizabeth into his arms but she couldn't help but feel that John was wrong. Kolya was alive; she knew it.

TBC…

Elizabeth might not know why she called her daughter Bree but I do and surprisingly it's actually got something to do with the story.


	8. Chapter 8

Disclaimer: I don't own Stargate Atlantis

Spoiler: Brief mention of 'The Gift'

Note: This is unbeta'd. Also updates may become slower since I go back to school on the 5th and then it is something like 5 or 6 weeks until my year stand down and start our final exams, which means for me a lot more revision and homework. When I get a little downtime I continue with this story but I may not get much.

**McCartney:** Is Kolya alive? I guess you'll just have to keep on reading because I am not telling you yet.

**Hazeydream**Have you been invading my mind? Those are the three ideas I originally came up with and I'll tell you now. One of them may be right.

**Ashkash: **First off, glad you liked chapter 6. I'm happy you found Johns' speech a little heartbreaking. Secondly glad you liked the second dream sequence. That originally wasn't going to be a dream at all, it was going to be something containing John and Liz but I decided against it.

**TubaPrincess: **Thanks, glad you like the name Bree.

**highonscifi**: Thanks, I hope this update is fast enough for you.

**

* * *

Atlantis **(Two days later)

Elizabeth looked out across the ocean. The waves lapped gently against the sides of the city.

Bree snuggled against Elizabeths' chest sleepily. Since her dream about Kolya taking her Elizabeth hadn't let Bree out of her sight. She'd even moved Bree's cradle into her room.

Elizabeth kissed the top of Bree's head.

"You know, he'll never find out about you and he'll never take you honey. I'd kill him if he ever tried to take you."

Elizabeth placed another kiss on the top of Bree's head as someone walked out onto the balcony.

The blonde haired woman stood next to her placing her hands on the railing.

"Elizabeth can we talk?"

Elizabeth sighed.

"Is that really necessary Kate?"

Kate turned to face Elizabeth. John had been right. Elizabeth did not want to confront this.

"Elizabeth, you've carried this around for nearly a year all by yourself. Why didn't you tell anyone?"

Elizabeth closed her eyes briefly before looking down at Bree.

"I didn't want to believe that he was alive because if I believe that I know there is a chance he could come and take Bree from me."

Kate understood. She knew how much Elizabeth loved Bree and how it would destroy her if anything happened Bree.

"Why didn't you tell anyone he was alive when you were rescued?"

Elizabeth sighed and tears fell onto her cheeks.

"Remember when you asked me if I loved him?"

Kate remembered. Elizabeth had been set in her decision that she didn't love him.

"I did. The woman he created loved him; she was part of me. She was the part that wouldn't let me tell anyone that he was alive. She's still there now. She's is what has kept me from telling people he's alive."

Kate put a reassuring hand on Elizabeths' shoulder.

"That doesn't necessarily mean _you're_ the one who loved him. You were programmed to be someone else."

Elizabeth shook her head.

"I often wonder why I allowed it to happen"

Kate was expecting Elizabeth to continue but instead she walked off the balcony back into the control room. Kate sighed and lent further onto the railing.

Elizabeth was breaking and Kate knew it. She knew it and there was very little she could do about, short of putting Elizabeth on 24-hour surveillance. Kate knew Elizabeth wouldn't hurt herself or do anything crazy, but she also knew that Elizabeth needed help, she couldn't keep everything locked up. It would end up destroying her.

* * *

Elizabeth into her office and put Bree in the Ancient equivalent of a playpen. She moved to her desk and began to type up reports. She could not believe Kate had come to psychobabble at her. Over the past two days it seemed like John had told everyone about her dreams. Earlier in the day before she went off world Teyla came to her quarters and offered to perform at ritual that was suppose to rid people of their nightmares. 

Elizabeth had snapped at the young woman and now she felt awful about it. Teyla was only trying to help after all. Elizabeth buried her head in her hands and sighed, she just wanted to forget about it. It was driving her crazy. Everyone was, yet again, assuming she was going to breakdown. She sighed, during the last year and half she'd completely lost control of her life. She wasn't the woman she used to be, Kolya had changed her permanently into someone else. Someone she'd never been. Elizabeth ran her fingers through her hair. She thought about how great it would be to just disappear. Go somewhere and never look back.

**

* * *

Off World **(Gistorri)

John, Ford, Rodney and Teyla walked down the long path to a small village on the planet of Gistorri. They'd made contact with them several days before and were going back to negotiate a trade alliance.

Actually, that was only half of it. The leader of the Gistorrians insisted that in order for a fair alliance to be made that would benefit both people he first must be able to trust them which meant he must go to Atlantis and meet with their leader. Elizabeth had not at all been happy with it but had agreed to it, which meant that John, Ford, Rodney and Teyla were going to retrieve him.

"Major Sheppard"

Jota, the leader of the Gistorrians greeted them.

"Jota, Good to see you again"

Jota and his high ministers bowed.

"As your leader agreed to our request?"

John nodded; he wasn't going to add that she agreed reluctantly.

"Yes, Dr Weir is looking forward to it"

Ford rolled his eyes. Last time he'd talked to Elizabeth, which was not long before they disembarked on the mission, she had not been happy about bringing complete strangers onto Atlantis. After her current dreams, she'd been viewing everyone as a threat. The only people she trusted where himself, John, Teyla, Rodney, Carson and Peter. Over the months of Elizabeths' pregnancy Ford had found himself becoming closer to Elizabeth. They'd become good friends and she began to confide in him. People had always thought she was closer to Carson but in reality Ford was the one she trusted most. He remembered back to the day she went into labour.

**Flashback **(4 Months earlier)

Ford knocked on the door to Elizabeths' office and walked in. Elizabeth looked up at him and smiled. Ford couldn't do anything but notice how she glowed and how beautiful it made her. Ford at down opposite her.

"How are you feeling Ma'am?"

Elizabeth smiled at him. He was glad to see her smile. In his opinion she didn't smile nearly enough.

"Aiden; I've told you before. Call me Elizabeth"

Ford smirked. She'd insisted for months now that he call her Elizabeth but rarely managed it.

"I'm fine, the baby as been kicking like crazy"

Ford sat forward.

"Is that normal? Are you both okay?"

Elizabeth smiled; she was touched by his concern. He really was a sweet kid.

"Aiden, it's normal. Don't worry"

Ford smiled, slightly embarrassed at how he overreacted. Elizabeth looked down at her laptop then back up at him, smiling nervously.

"So, how is John? I haven't really talked to him recently"

John had been spending a lot of his time recently either at the Alpha site or on the mainland and although they did talk to each other, it was mostly about work. When they did talk about other things, it was usually very brief.

Ford was certain that John had heard the rumour that Elizabeth and Carson were more then friends but anyone close to them knew it wasn't the case. Carson was being supportive but nothing else. Everyone knew Elizabeth still had feelings for John. Her question proved she did.

"He's fine. He's on the mainland."

Elizabeth nodded.

"He's been there a lot lately."

Ford instantly knew what she was saying. A rumour was going around Atlantis that John had started a relationship with one of the Athosians' and Ford had done his best to try to keep it from her but it appeared that someone had outsmarted him and told her that it was true.

"Elizabeth. That rumour you heard is not true. John is not seeing anyone."

Elizabeth smiled nervously.

"Its' none of my business if he is."

Ford smiled sympathetically.

"Elizabeth, it's okay if you still feel something for him."

Elizabeth smiled and her eyes filled with tears.

"I wouldn't really blame him if he was."

She placed her hands on her abdomen and closed her eyes.

"Elizabeth…"

Elizabeth winced in pain.

"Elizabeth, are you okay?"

He walked around to where Elizabeth was sat.

"C'mon, I'll take you to the infirmary."

Elizabeth shook her head.

"No, I'm okay"

Ford wouldn't take no for a answer though. He helped her from her seat and took her down to the infirmary.

**End of Flashback**

The team, along with Jota and the high ministers walked back to the Stargate. They walked through the Stargate half-expecting Elizabeth to be waiting for them. Instead, she was in the office oblivious to the fact that they'd even stepped through the 'gate. John shot a 'wait here' at his team and run up the stairs to Elizabeths' office.

"Liz, Jota and the high ministers are here. It does not look good that you're not there waiting for us."

Elizabeth looked up at him then glanced to the playpen opposite her.

"I'm not leaving her in here by herself."

John walked over to the playpen and picked up Bree.

"I'll take her, you don't need me for this thing do you?"

Elizabeth sighed.

"I could use you, look ask Aiden if he'll take Bree."

John nodded. Elizabeth switched off her laptop, straightened herself and followed John down the stairs. John walked over to Ford.

"Lt, will you take Bree?"

Ford nodded and took Bree into his arms and began rocking her off to sleep gently.

Elizabeth walked over to Jota and the high ministers.

"Jota, this is Dr Weir"

Jota took Elizabeths' hand and kissed it.

"Dr Weir it is honour to meet you."

Jotas' gaze drifted to Bree.

"Is that your daughter?"

Ford noticed how uncomfortable Elizabeth became.

"Yes."

She answered nervously and gave Ford a look telling him to take Bree away.

"We better go down to the infirmary."

Ford glanced at Teyla and Rodney and they understood.

"Yeah we should"

Rodney murmured and began to walk in the direction of the infirmary followed by Ford and Teyla.

Jota watched them go and turned back to Elizabeth.

"You have a very beautiful daughter."

Elizabeth nodded

"Thank you. We should really start this meeting"

Elizabeth gestured to Bates and they followed him to the briefing room. John stopped Elizabeth from following them and whispered

"Are you okay?"

Elizabeth avoided his gaze.

"I don't like the way he took such an interest in Bree."

John shook his head.

"He was just being friendly. He's not a threat Elizabeth"

Elizabeth nodded and walked up to the briefing room.

* * *

The meeting ended several hours later with an invitation from Jota for Elizabeth, John, Bates and the rest of SGA1 to attend a celebratory banquet on Gistorri. John couldn't help but notice that Elizabeth looked more relaxed with them. 

"We would love to come."

Jota smiled happily.

"The banquet shall take place in two days. Until then"

Jota and the high ministers bowed their heads and began to leave through the Stargate. Jota turned to them.

"Dr Weir, your daughter is more then welcome to attend also."

Elizabeth smiled nervously, she wasn't in a position to trust many people and this guy's interest in Bree freaked her.

"Maybe"

Jota smiled at her before stepping through the Stargate.

**Off world **(Gistorri)

Jota walked into his house. He moved over to a drawer and took out a radio.

"Relay station three, prepare to receive transmission."

A voice came over the radio.

"RS three, awaiting transmission"

Jota smirked.

"Let Cowen of the Genii know, we have found her."

Jota smirked. The search was over.

TBC…


	9. Chapter 9

Disclaimer: I don't own it.

Note: Recently been having trouble with this but I think I've finally figured everything out now. I've been writing this slowly during school time so please forgive me for taking so long to upload this. Thanks to Patricia for Beta reading.

**Sydney Bristow: **I try not to be mean.

**Highonscifi: **Thank you. Those Genii are pesky aren't they?

**ErabuHikari: **Um, I guess I forgive you. Glad you like the story.

**Quezacolt: **All shall be revealed soon.

**Ashkash: **Thanks, I really like Fords' character and I hate that they haven't explored him further, so every time I write a fic I try and incorporate Ford somehow.

**Rhin Ariel: **Yeah thank you. Glad you're enjoying it.

**TubaPrincess: **I leave chapters like that so you come back again. Glad you like the Ford flashback.

**Hazeydream: **I'm not going to tell you if Kolya shows up. Glad you like the flashback.

**Wolfdream**I leave it with a cliff-hanger because I want you to come back for more. Glad you like the story. And once again, I'll say 'Make 'Weathering the storm' a John/Liz fic, I'm begging you.

**

* * *

Off World **(Gistorri)

Elizabeth, John, Bates and the team walked through the Stargate and were met by the Gistorrian High ministers and Jota.

Jota smirked as they came through the event horizon but his smirk quickly disappeared when he saw Bree was not with them. That seriously damaged their plan.

"Dr Weir, Major Sheppard. It is good to see you both again. Dr Weir, did you not bring your daughter with you?"

Jota covered up the bitterness and anger in his voice and smiled at Elizabeth. Elizabeth smiled back at him still slightly unsettled by his interest in Bree.

"I thought it best not to put her through Stargate Travel while she's so young."

Jota gritted his teeth and nodded.

"I understand, but believe me. It is harmless to everyone."

Elizabeth nodded

"Well, maybe next time"

Jota couldn't help but notice the sarcasm in her voice. She didn't trust him, he was going to have to change that. He needed her to trust him fully before his special 'guests' arrived.

"Please come with me and I will take you to the town hall to finalise our arrangement then we shall proceed to the banquet hall."

Jota led them away from the Stargate knowing fair well it may be the last time any of them saw it.

**Off World** (Genii Home world)

Cowen smirked as the Genii Stargate connected to the Gistorrian Stargate.

He watched as a full company deployed through the Stargate .They would lie in wait until Jota gave the signal then they would execute their plan. Cowen watched as the final member of the company walked through, he turned to the man standing next to him.

"I could do this for you. If your wounds are not fully healed."

The man shook his head and walked through the Stargate without looking back. The Stargate shut down, Cowen sighed, she was essential to their very survival and Cowen just hoped that he would not let his emotions get in the way of their objective.

**Off World **(Gistorri)

The Gistorrian High Ministers and the Atlantis team sat at the banquet table.

"We give thanks to the Ancestors for bringing these new trading partners to us."

Jota raised his glass and everyone else followed suit. Jota, who had insisted on sitting next to Elizabeth, turned to her.

"I hope both parties can live up to this Alliance"

Elizabeth nodded.

"I hope we both…"

Before she could finish her sentence, she slumped down onto the table, John, who was sat on the other side of her, instantly reacted.

"Elizabeth"

He saw a dart sticking out of Elizabeths' neck and quickly pulled it out. He looked around the table and saw that the rest of the team were also drugged. He then felt the smooth cold metal of a gun against his neck.

"There are over 60 guns pointed on you Major, 61 if you include my own. Make no sudden movements or I will pull the trigger and blow your head off, and believe me, I'll have no trouble in doing that."

John knew the voice, but it couldn't be, but John knew it was totally within the realm of possibility if what Elizabeth said was true.

"Kolya"

The gun pushed itself against his neck harder and he could hear the safety being taken off.

"I should thank you for the supplies we took. This handgun as you call it is a lot more effective then our own guns."

The gun moved off his neck and John began to move to grab his own handgun.

"I wouldn't make any sudden movements Major, remember, over 60 guns are pointed on you and your people."

The man moved around the table and John saw him for the first time as he walked over to Jota, it was Kolya.

"We owe a great reward Jota, to both you and your people"

Johns' head shot up to face Jota who had a smug smirk on his face.

"Where is the child Jota?"

John tensed as he heard the mention of a child and knew he was talking about Bree. Jotas' smug smirk fell.

"She is not here."

John watched as Kolya filled with rage.

"Are you saying she is still on Atlantis?"

Jota nodded nervously.

"Yes, but they have a valid IDC. We can use it to drop the Atlantis shield."

Kolyas' gaze dropped over the Atlantis team. Teyla, Ford, Rodney and Bates, all of them were still unconscious and helpless. His gaze dropped to John, a look of disgust on his face.

"Lock them up"

The guards grabbed the five members of the team and as one of the guards went for Elizabeth, Kolya stopped him.

"No, leave her. I will deal with her first,"

John looked at Kolya as he was taken away. He saw the dark coldness in his eyes and John was, understandably, scared for Elizabeth, and Bree.

(Gistorri) _Several hours later_

Ford moaned as he rolled onto his side and bumped into someone. He quickly opened his eyes and saw John sitting next to him, staring into the distance unaware that Ford had even bumped into him. Ford quickly looked around and saw Bates, Rodney and Teyla all waking from their slumber.

"Sir, what happened?"

John turned to him.

"Jota used us. The Genii are here."

Ford saw the blank expression in the Major's eyes and he finally registered that Elizabeth was not with them.

"Sir, where's Dr Weir?"

John closed his eyes, fighting back the tears, which were forming there.

"Kolya has her."

Ford didn't think he'd heard him right but when the tears fell down his cheek he knew it must be true because John Sheppard never cried. John furiously pushed back the tears and turned to Ford.

"He's alive, Elizabeth was right."

* * *

Kolya circled the room and stared at the woman tied in the chair. She was still unconscious, the dosage they'd used on her had been higher then the one used on the rest of the team. He slowly walked over to her and ran his fingers through her hair as she slowly awoke, light filled her eyes and blinded her. 

"My dear Elizabeth. I have missed you."

Elizabeth looked up at him and as her vision came into focus and she saw who was in front of her panic overtook her. Kolya tenderly placed a kiss on her cheek.

"Tell me, how is _our _daughter? How is _Bree_?"

Elizabeth froze as she heard him say Brees' name.

He knew.

But how could he?

TBC…


	10. Chapter 10

Disclaimer: I don't own Stargate Atlantis.

Note: Thanks to Patricia for Beta Reading.

**Espiritu:** Thanks glad you're enjoying this and here's the next part.

**TubaPrincess:** Thanks, I'm glad I was able to finish it as well.

**Crossbecca: **Don't worry I'm not ending it there. Glad you're enjoying it.

**ErabuHikari: **I'm glad you think this is getting exciting.

**Ashkash: **Want violence and anger? There is some more in this chapter.

* * *

A million questions rang through Elizabeths' mind as she heard Kolya say Brees' name. A million feelings cut her up inside. Fear, pain, resentment. She wanted to know how he knew about Bree, what he'd done to the rest of the team. Whether he already had a team on Atlantis taking Bree. But she didn't falter, not once. Didn't show him the fear he strived to see. 

Kolya knew what she was doing, she'd done it before. Those first few months she'd been captured she showed no weakness, she didn't let him break through. But it had been so rewarding when he finally had broken through her tough outside. Made it so she would break down in his arms so he could _comfort _her.

**Flashback **(1 Year, 5 Months earlier)

Elizabeth quivered on the floor of her cell; silent tears of pain ran down her face. She was breaking, but she didn't realise it. Didn't realise all the work Kolya was putting in to brainwash her was working. She sat against the wall and drew her knees into her chest, not even registering the pain that was coming from her ribs. She gently rocked back and forth wiping the tears from her eyes. She strived to see someone she knew, anyone that could offer her comfort. She just wished she could go home, Atlantis or Earth, she didn't care. There were people on both that cared for her. John on Atlantis cared for her, so did Carson or did they, they were friends but did they see her as important to them…Earth, were Simon was, reliable, loving, overprotecting, jealous and not the way she had originally pictured him, that was how she knew their trip home was a fake. The spark was there, a spark that had never been there passed between them…He didn't love her. No one really loved her.

Tears fell freely from Elizabeths' eyes as the door to her cell opened and someone walked in. She was too tired to go through another beating again.

She closed her eyes, hoping that they would believe she was asleep. Instead someone sat next to her and drew her into their arms.

She cautiously opened one of her eyes and saw they face of the person who was comforting her.

Kolya.

She moved away from him, but after weeks and weeks of beatings she was too weak and fell back into his arms. He gently shushed her and rocked her gently.

"They don't care for you Elizabeth; if they did they would have rescued you by now. Like they did with Dr McKay. I didn't want to tell you this but they rescued him a few weeks ago. But they didn't come for you. I'm the only person you can trust Elizabeth. I'm the only person who cares for you. As soon as you begin to realise that you'll feel much better and you can get on with your life."

She tried to struggle away from him, tried to tell herself what he was saying wasn't true. That they'd come for her, take her back to Atlantis but Kolyas' words cut through her, deeply, they hurt her.

"You're lying"

Her voice was barely above a whisper but Kolya heard it. He placed a sweet kiss on her forehead and drew her in closer.

"I wish I were, but you'll realise I'm the only one who loves you."

He kissed her cheek, stood up and left the room. Elizabeth dropped her head against the wall and let her tears fall free. She didn't want to believe Kolya, she wanted to hate him, but maybe he was making sense, maybe he was the only one who cared for her. Maybe he was the only one who did…love her.

**End of Flashback**

The memory hit Elizabeth like a million knives stabbing her all over her body. Kolya knew the memory was hurting her. His own memory of what he put her through sometimes hurt him, to think of how he allowed her to be beaten just so she would open up to him so he could manipulate her. He walked over to her and gently ran his fingers through her hair. Elizabeth sharply turned her head away from him. Kolya grabbed her chin and forced her to face him. He ran his hand down her cheek and cupped it. Without warning he lent in and deeply kissed her.

As his mouth connected with hers Elizabeth felt sick. She wanted to cut out her tongue as he brushed it with his. As he bit her lip she could taste the blood flowing freely from it. Kolya moved away from her mouth but stayed close enough to lick the blood from her wound and then he sucked her lip to clot the blood. As Kolya moved fully away from her she spit out the blood that was still in her mouth and she tried to spit out the taste of him. Kolya stood in front of her, watching this beautiful woman try to rid herself of the taste of him. He chuckled quietly and kissed her forehead again before grabbing a chair from the corner of the room and placing it in front of her. He smirked at her.

"So Elizabeth, you haven't told me; how is our daughter?"

Elizabeth closed her eyes and turned away from him hoping if she ignored him enough he would go away. Kolya tenderly touched her cheek and forced her to look at him. Tears threatened to fall from Elizabeths' eyes. She just wanted to go home to her daughter. To just curl up in Johns' arms. Kolya drew his finger down her cheek casually.

"I'm sure you're interested to know how I know _our_ daughters' name is Bree. You might not remember this Elizabeth. It was something I incorporated into your programming just in case you were rescued. I didn't want you to remember some details of the Genii. I didn't want you to inform Major Sheppard of our most secret plans. Anyway, Bree is such a pretty name isn't it."

**Flashback **(1 Year, 3 Months earlier)

Kolya kissed Elizabeths' neck tenderly as she moved her head to give him better access. There was no doubt in his mind that the training had worked perfectly. She believed that she was Elizabeth Kolya of the Genii and that she was married to the loving Commander Acastus Kolya of the Genii. Kolyas' grip tightened around Elizabeths' waist and she relaxed into him.

"Keep doing that"

Her voice was filled with passion and lust and Kolya responded by placing more kisses on her collarbone. Kolya drew his hand across Elizabeth abdomen and she sighed knowing what he was about to suggest.

"You know what would make this perfect. A child."

Elizabeth sighed and moved away from him, pissed that he had just spoilt the moment.

"I cannot believe we are talking about this again"

Despite all the programming Kolya had managed to do on Elizabeth, he still hadn't been able to change the fact that she didn't want children.

"Elizabeth my darling, I am just saying that I think you would make an excellent mother and I want to see that."

Elizabeth shook her head and stood up.

"Elizabeth…" Kolya stood up and ran his fingers through her hair.

"Imagine what she would look like, your eyes, your hair, hopefully your mind. She would be such a smart little girl; she would grow up a warrior. We could name her Bree, after your mother."

Elizabeth shook her head.

"I do not want children."

Kolya sighed and shook his head.

"I want children Elizabeth, and I want children with you. My darling"

Kolya gently kissed her, drawing her into his arms.

"Think about it."

Elizabeth sighed and reluctantly nodded.

"You should be resting Acastus, that bullet wound needs to heal quickly"

She danced her fingers across his torso just above his heart.

"I nearly lost you."

Kolya kissed her forehead and dragged her to sit down with him.

"You'll never lose me Elizabeth. I shall always be with you my love."

**End of Flashback**

Elizabeth listened to his words and was shocked by the memories, which invaded her mind. Her love for Kolya. His supposed love for her. She choked back the sobs, which were threatening to take complete control of her.

Kolya bent down in front of her.

"Despite what you may tell yourself, you loved me Elizabeth, I suspect you still do; and you love _our _daughter."

Elizabeth turned her head away in disgust, how could he even suggest that she was the one that loved him and that she still loved him. Elizabeth pushed back her tears and disgust and faced him.

"I never loved you, I don't love you now and I will never love you"

It was the first thing she'd said to him since seeing him and she said it with confidence and strength. She wasn't scared of him, she couldn't be scared of him.

Her words seemed to hit Kolya, despite his insistence that he didn't feel anything for her he couldn't help but still feel enthralled by her presence and her strength. It had what had attracted him to her in the first place.

Kolya swallowed hard.

"What about Bree? Do you love her?"

Elizabeth loved Bree, of course she did. Bree was her daughter, her little girl.

"Of course I love her, and do you want to know why? Because she reminds me nothing of you"

Kolya lowered his head. Elizabeth couldn't tell whether she'd pissed him off or upset him. He looked back up at her and smirked.

"Where is Bree now? Is she on Atlantis?"

Elizabeth kept quiet. There was not a chance in hell she was letting this bastard at her daughter. Kolya simply smirked at her silence.

"So she is on Atlantis."

Kolya put his hand into his pocket and took out a GDO.

"I want you to put your code in here and drop the Stargate shield."

Elizabeth couldn't help but laugh, she didn't mean to but she couldn't believe he thought she would actually help him take her daughter away from her.

"No, not a chance in hell."

Kolya, in one swift movement, dragged Elizabeth from the, threw her against the wall and kissed her roughly.

"Do I need to remind you what I am capable of?"

Elizabeth felt the gun that had connected itself to her ribs but it didn't scare her one bit because she knew Kolya wouldn't kill her or hurt her.

"No, I know exactly what you are capable of, murder, torture, rape. I remember far too well; and let me tell you that's exactly why you'll never set eyes on Bree."

Kolya became enraged and threw her to the ground. Elizabeth connected with the ground hard and had the wind knocked out of her. She took a deep intake of breath before turning round. As she turned round, she saw Kolya looming over her. He dragged her to her feet and threw her back into the chair and tied her up tightly again. As he stood up, he placed his hands on her shoulders.

"I'm sorry Elizabeth, if I hurt you just now. I didn't mean to. Please forgive me."

Elizabeth shook her head in disbelief. What was he trying to do? Was he trying to programme her again?

"I just get so upset when people mention Bree, having never seen her I get upset."

Elizabeth pushed away the pang of sympathy that was building up in her. No, it wasn't going to work. He wasn't going to use her daughter to manipulate her.

"How would you feel Elizabeth? If you'd never seen your daughter? You'd be desperate to see her, I know you would. That's how I feel my darling. I just want to see my daughter"

No, there was more to it then just seeing Bree and Elizabeth knew that. He wanted Bree for something. It was something to do with the Genii. She could hear it in her mind, but she couldn't make out the words.

TBC…


	11. Chapter 11

Disclaimer: I don't own Stargate Atlantis

Note: I'm so sorry you've had to wait for this but I usually write during lunchtime at school but lately I have been locked in the drama studio working on my final year performance meaning I haven't had much time to write. Please note it's not beta'd.

**TubaPrincess**Yep Kolya is a Jerk, I'm not going to tell you _yet_ what he wants her for.  
**Ashkash**Just so you know it is quite possible Elizabeth says something along those lines.  
**Quezacolt** Don't worry, Kolya and John will come to blows soon.  
**Crossbecca: **Thanks for reviewing; I'm glad you like it.  
**ErabuHikari**: Awww, I'm glad you hate him, but strangely since I've been writing him I've started to like him, I'm joking.  
**Wolfdream**Hope you keep reading, glad we've sorted out the intertwining stories.  
**Hazeydream** Thanks, glad you like this.

* * *

Kolya watched her from a distance; he saw her struggle to regain her memories with the Genii. He saw her trying to deal with her feelings as he tried to deal with his own. He didn't want to hurt her, he couldn't bare to see her hurt, but he needed his daughter. The Genii needed her. 

He knew Elizabeth didn't trust him, that much was obvious, to be honest if he was in her position he wouldn't believe himself either. Kolya smiled, her strength was amazing, she wouldn't be easy to break, but he'd still try and if that failed, there was always John Sheppard.

* * *

Ford winced as John kicked at the door again. Ford had tried to convince him it was a waste of time trying to kick the door down, but he just didn't want to listen. Ford shook his head and grabbed Johns' arm. He pulled him back and stared at him. 

"That is not going to help the situation…sir"

Ford didn't like being disrespectful, especially to John but he knew that his CO had to stop being ruled by his heat and start being ruled by his head.

John looked at Ford.

"I'm sorry."

He looked round at Bates, Teyla and Rodney.

"I'm sorry"

Ford nodded and looked at the group, they were all silent, they all knew John wasn't thinking straight and all quietly awaited Fords' orders. Ford would not do that; he would not overrule his friends' command. Ford moved and stood with the group. Ford trusted John, he trusted he would do what was right, he gave him a nod, an understanding that he would follow Johns' orders regardless of what they were.

John looked at Ford; he was the trust that passed between them. John wanted to do everything possible to get Elizabeth back; he also knew that Ford would step in and tell him if he was going too far, if his judgement was impaired. John trusted Fords' ability to command but this was his fight and Ford knew that.

John turned to the group and cleared his throat.

"We I have a plan, rescue Elizabeth and preferably liquidate Kolya, remember it's Elizabeth so we'll have to be careful but don't let your heart control you; any of you."

Teyla gave him a warming smile indicating that she would follow his orders and that she trusted him. John smiled back, grateful he had both Teyla and Ford on his side. He was expecting Bates to be an ass but what he was met with surprised him.

"Yes sir"

Rodney didn't say anything but he gave John a nod, a nod that told him that he was on side.

John smiled and turned to the group.

"Okay, this is what we're going to do."

* * *

Elizabeth shut her eyes and tried to block out the voice that was Kolya and his attempts to convince her that he wasn't going to hurt her, that he knew she was still in love with him and he was with her. 

As hard as she tried to stop him, he was slowly chipping away at her and getting under her skin, making her remember that woman she was with him, as much as she tried to push her away, she kept rising threatening to surface.

"Elizabeth, my dear, all I ask is for you to let me see my daughter, it is my only request."

Elizabeth knew he had ulterior motives, that voice at the back of her head which screamed logic was in full force telling her that he was going to try and take Bree and she trusted that voice.

Kolya bent down in front of her and cupped her cheek.

"My Darling, please do not deny me the chance to see my daughter."

Elizabeth shook her head and was met with Kolyas' lips invading hers, he then stood up and walked to the door.

"I will give you some time to think about it."

Kolya walked out of the door leaving Elizabeth alone, trying to compose herself.

As soon as the door shut she let out the tears she'd been holding in, she choked back the sound of her sobs as not to alert Kolya, she would not let him know he was getting to her,

_That's exactly what he wants and I am not going to give him the satisfaction. _

She fought with herself and finally stopped the tears and the sobs. She had to work on getting out of here, not on feeling sorry for herself. She was going to have to gain his trust, there was only one way she could do that and it was not a way she was looking forward to. She closed her eyes and sighed

_Please forgive John._

* * *

A few moments later, the door to Elizabeths' cell swung opened and Kolya walked in. 

He walked over to her, dragging a chair behind him and sat down in front of her.

Elizabeth took in a deep breath,

"Have you thought about what I said?"

Elizabeth nodded.

"I wish you'd just tell me what you want Bree for, that's all, if I knew you weren't going to hurt her…"

Elizabeth trailed off and looked down; she waited to see if he would take the bait. She waited patiently and she eventually felt Kolyas' hand on her chin as he lifted her head to face him. He removed his hand from her chin and placed his around her cheek.

She saw his eyes soften as he pressed his lips to hers. Elizabeth instantly felt sick as she gradually responded. She knew it was necessary to protect Bree but it also was sickening and degrading as if she was condoning the fact that he raped her.

She tensed as he forced her to stand, slipped his arms around her waist and pulled her into him. She heard him moan as he slipped his tongue into her mouth.

Elizabeth couldn't take anymore and pulled her mouth away from his.

When Kolya came into the cell and saw Elizabeth he smirked, she was still as beautiful as always, he was still attracted to her but he wouldn't let that effect his judgement though or let this mission fail.

When he saw the look in Elizabeths' eyes when she was talking about Bree he saw the look his wife used to give him, his Elizabeth Kolya, it was love.

As he lifted her chin and saw her eyes again he was overcome by feelings of desire. He placed his lips to hers, waiting for her to push him away, when she responded his feelings overtook him, he dragged her to her feet and pushed his hips onto hers. He wanted her so badly, he moaned and slipped his tongue into her mouth. He reluctantly released her tongue when she pulled away.

The two of them looked at each other, Elizabeth was feeling sick and ashamed of herself while Kolya was beginning to believe he'd won her round, that she would take Bree and go back to him.

Deep down he knew it was a long shot to think Elizabeth was falling back in love with him but he wanted to believe so much since she'd left, wanted to believe it wasn't just the programming that cased her to love him. It had consumed him at one point. When he woke up and found she was not there he revealed to Cowen the truth about Elizabeth, about what she meant to the Genii.

**Flashback **(Genii home world 8 months ago)

Kolya opened his eyes and slowly looked around the room, he could see a woman stood near the bed, his vision was blurred causing the woman to look distorted.

The woman walked nearer to the bed.

"Elizabeth?"

His voice was cracked and broken, as the woman walked nearer he saw who it really was.

"Sora?"

His vision became clearer and he saw the blonde place a cold, wet towel to his forehead and cheeks. She picked up the cup of water next to his bed and placed it to his lips.

"Here, take small sips"

He slowly sipped the water and then Sora placed the cup back on the table next to his bed. A few moments later Cowen walked into the room, told Sora to leave and sat down next to the bed.

"How are you feeling Acastus?"

Kolya coughed slightly before responding.

"Where is Elizabeth?"

Cowen shook his head and sighed.

"Elizabeth is gone; your programming did not work."

Kolya tried to sit up ignoring the pain in his chest. Cowen sighed again and rose to help him.

"Major Sheppard shot you; it will take a while for you to heal"

Kolya lent back in the bed. He closed his eyes before speaking.

"We need to find Elizabeth."

Cowen shook his head sympathetically.

"She is gone Acastus, you must accept that. A team from Atlantis took her, they made her remember who she really is."

Kolya shook his head.

"She is pregnant, I am sure of it"

Cowen looked at Kolya in disbelief, how could he be so stupid to father Elizabeths' child. Cowen stood up furious.

"How could you be so stupid? You knew there was always a chance they would come for her, what were you thinking?"

Kolya looked down, how could he tell Cowen his feelings for Elizabeth, the woman he held captive. It wasn't only that he had feelings for her, there was something else, something Cowen wouldn't be happy about.

"There was a reason behind it, the child is prophesied, it would have happened anyway."

Cowen looked at him in disbelief.

"Prophesied? How do you know it was her, how can you be sure? This child may not be the one"

Kolya shook his head, he knew Elizabeth was the one, he knew this child would be the one to deliver them from the Wraith.

"I know because I know, everything lined up, the date she was taken, the date the child was convinced even the fact that the mother would have connections to the Ancients."

Cowen shook his head, he knew of the prophesy, all Genii's knew about the prophesy that a child would come and deliver them from the Wraith. They all knew that the child would possess the greatest power, the power to sense the Wraith and the ability to fight the Wraith.

"It is Elizabeth; the mother of the child was prophesied to be able to sense when her people were in danger, if Elizabeth was there when I got shot she must have sensed I was going to be in danger, it makes sense."

Cowen shook his head.

"We can not retrieve the child if Elizabeth is actually pregnant, it would be too dangerous to go onto Atlantis, we have allies who could help us, we could lure them to off world either while she is still pregnant or after the child is born. It would be dangerous but if this is the child is the one then we must do everything in our power to retrieve it."

Kolya looked at him sharply, he did not want people calling his child an _it_, the child was more then that to him, more then just a saviour, he knew the child would be a girl, he knew she'd look like Elizabeth and he would love her unconditionally.

He just needed to find her

**End of Flashback**

Kolya released Elizabeth from his grip and let her sit back down. Elizabeth looked down trying to compose herself. She felt dirty, she just wanted to wash away his touch and his taste, but she couldn't let him know that, she had to make him believe she was beginning to him. She felt sick when she realised the lengths she might need to go to prove it.

TBC…


	12. Chapter 12

Disclaimer: I don't own it.

Note: For those who wanted it, there will be a small fight Kolya and the lovable and yummy John.

Spoilers: I know I said up to season 2 originally I'll remind you again because there are major spoilers for 'The Defiant one' and 'The Gift'

**Ashkash**Remember that line you were waiting for? (check chapter 10 review). Well you might be in luck. The prophecy is explained more in this chapter. Glad you liked Aiden's input; expect more of him in this chapter.  
**TubaPrincess**: A few of my friends who have read bits of the story for me (they don't want Atlantis) have told me they feel a bit sorry for Kolya too. All we have to remember is that he is a jerk.  
**Hazeydream**: Glad you liked the part with Aiden. I was actually a bit worried about that a first.

* * *

Elizabeth had done a lot in her time, some things that made her proud. Some things she was ashamed of.  
What she was doing right now fell into the ashamed category,  
She was allowing Kolya to push her firmly against a wall and kiss her, his lips dropping from her lips to her neck.  
Her conscious was screaming at her to make the insanity stop. To tell Kolya he was a pathetic rat bastard who nobody would ever love especially her but her logic was telling her this was the only way to ensure Bree's safety.  
And a small part of Elizabeth, the part which she tried to keep locked away was enjoying the sensation. Enjoying Kolya's lips making their way down her body, enjoying his hips pressed against hers so she could feel how much he wanted her.  
That small part was Elizabeth Kolya and unknown to Elizabeth that small part was getting stronger, threatening to consume her. 

Logic was screaming at Kolya telling him that this was insane, that Elizabeth had ulterior motives, but to feel her respond to him like she used too, it pushed away any doubt in his mind and he pushed her harder against the wall, hearing her moan as he did.  
Little did Kolya know that his weakness for Elizabeth could be his downfall.

* * *

John and his team had a plan, all the needed was to put it into motion. John knew that Kolya had Elizabeth. He also knew Kolya wanted Bree. 

There was a small window in the door that John had been kicking earlier. The small window had factored nicely into their plan.  
John walked over to the door and began to bang on it.

"Jota, I know you can hear me. Open the door you lying, cheating bastard."

The small window opened and someone looked in. John could tell it was Jota.

"Finally. You know Jota; you should work on how you treat guests. The service is…kinda crap."

Jota hissed at him through the window.

"What do you want?"

John sighed as if in thought.

"Ideally to kick your ass for lying to us you piece of scum but you know if that's not possible I'd like to see Kolya."

"The great Commander Kolya had asked not to be disturbed"

He spoke as if in admiration of Kolya.

"Well tell _the great commander Kolya _that I have something of value to offer him."

Jota hissed again before closing the window.

When he was sure Jota had gone he turned to his team and spoke to them in a hushed tone.

"Okay guys, chances are guards will come in to get me and they'll come in armed. McKay…" He turned to his friend. "…I need to know you can do this right. You have to be convincing."

"You have my word John. I will not screw this up."

John knew how much Rodney loved both Elizabeth and Bree. He knew Rodney would do this to the best of his ability.  
John nodded and smiled at his friend.

* * *

The door to Elizabeths' cell opened and Kolya quickly let Elizabeth off the wall. 

A guard came into the room. If he noticed anything amiss, he didn't mention it

"Commander Kolya. Jota has informed me Major Sheppard wishes to speak with you."

Kolya looked at Elizabeth with suspicion. She didn't even need to look confused. She had no idea what John was up to. She just hoped he didn't get himself or his team hurt.

When the guard left, Kolya pressed his lips to Elizabeths' in a long passionate kiss.

"I will return soon."

Elizabeth watched Kolya leave the room. When she was sure Kolya was gone, she slid down the wall and buried her head in her hands. Her whole body was shaking with fear and betrayal. She felt as if she'd betrayed herself, her daughter and John. She pushed back her sobs and stood up.

She couldn't be weak now. John had a plan and she knew she somehow factored into it and she had to be there for him.

* * *

The door to the cell that held John and his team swung open. Ten armed guards walked into the room, their guns pointed on the team while Jota came in and grabbed John. 

"You come with me"

As he began too drag John to the door, Rodney fell onto the floor and began to convulse.

"Dr McKay"

Teyla tried to go to Rodney but a guard stopped her. She turned to the guard.

"He needs help"

Jota nodded at two of the guards and they went over to McKay and bent down beside him.

John nodded to the rest of his team before quickly grabbing Jota by the neck and grabbing his gun. This gave Aiden and Bates the opportunity to overpower the four guards around them while John, who still had Jota by the neck quickly took out the guards by McKay and Teyla.

John then put the barrel of the gun on Jotas' head.

"Alright you smarmy bastard; where is Elizabeth?"

Jota struggled against John but his grip was too strong.

"I shall not betray the great Genii race. They will rid you from existence."

John tightened his grip.

"Don't make me kill you."

Jota began to hose under Johns' grip; he coughed and choked out.

"I will take you to her; I will take you to her."

John loosened his grip slightly.

"That's good, now, where is Kolya?"

Jota looked down.

"He is waiting for you in a nearby room. Down the corridor."

John pushed Jota over to Aiden.

"Make sure he takes you to Elizabeth. If she's hurt…"

Aiden cut him off.

"…I know sir"

John looked over at McKay, who was now stood up.

"Good job Rodney"

John headed out of the room and down the corridor while Aiden pushed Jota out of the cell followed by the team.

* * *

Elizabeth took a deep breath as the door to her cell opened. She prepared herself. She didn't know what John had done but she had a feeling Kolya would be pissed. 

She slid down the wall and began to breathe heavily. She couldn't do it again.  
She couldn't pretend she was in love with that bastard. She placed her head in her hands as she heard footsteps approaching her. She felt a hand touch her knee.

"Dr Weir? Elizabeth?"

Elizabeth lifted her head and looked into the kind brown eyes of Aiden Ford.

"Aiden?"

She sighed in relief and lent into Aidens' arms. Aiden held her tightly; the realism hit him that they could have come close to loosing her again. That Kolya could have done anything to her.

"Elizabeth are you hurt?"

Elizabeth shook her head and pulled herself gently from his arms. She smiled at him with thanks and looked around the room.

"Where's John?"

* * *

Kolya sat calmly on a chair in the middle of the dark damp room. He was curious about what Major Sheppard wanted to talk to him about but Kolya was determined to make the Major pay for trying to take his daughter from him. He'd heard from Jota that Major Sheppard seemed to have taken the role of father and Kolya was not happy about that. Bree had only one father and it would never be Sheppard. 

Kolya stood as he heard the door open. He was expecting Jota to walk in with John but instead he saw John come in. Eyes blazing with anger and rage. A gun pointed straight at Kolyas' head. John walked further into the room, his aim never wavering.

"Don't move you bastard. Try anything and I'll put a bullet through your skull without a second thought"

John gestured the chair that Kolya had just left.

"Sit down"

Kolya gave John a death glare before sitting down. John moved over to Kolya slowly picking up a piece of robe. He intended to tie Kolya up and get the answers he wanted. He needed to know why Kolya wanted to harm _his _family. The people he loved.

As John reached Kolya, the gun was knocked out of his hand and he was thrown to the ground.  
He quickly turned round and saw Kolya lunging over him. Thinking fast John quickly swung his legs and kicked Kolya's legs from underneath him.  
Kolya fell to the floor with a loud thump.  
John quickly retrieved a knife from his vest pocket and moved over to Kolya, placing the knife to his neck, nipping the skin causing a few drops of blood to fall from the wound. John started to press the knife into his soft fleshy skin. Just as he was about to finish it, end Kolya's worthless life, he felt his arm being pulled back.

John turned round and saw Elizabeth dragging his arm away, a begging look in her eyes.

"John let him go. You're not a murderer. Give the knife to me."

John closed his eyes and pulled the knife away from Kolya's neck. He handed the knife to Elizabeth and stood up.  
Kolya began to rise to his feet when Elizabeth knocked him back down to the ground in a quick sweep placing the knife back to his neck.  
Kolya was in a moment of shock but then it all fell into place; she used him, to gain his trust. The clever little vixen.

"You ever, ever come near me, my daughter or my people again I will kill you, I promise I will end you're pointless and worthless life. I don't care what you need _my _daughter for; I will never let you near her."

Tears pierced her eyes but she held her ground. John, who had recovered for his moment of shock grabbed Elizabeth and forced her to stand. Elizabeth stood up, her eyes still on Kolya and she immediately gave John the knife. She began to walk out of the room when Kolya's voice stopped her.

"One day, you'll discover her power; discover how important she is to the Genii race. One day Elizabeth, you will come to me for answers."

Aiden, who had been stood ay the doorway listening, who had seen the look on Elizabeths' face when he found her, who saw that look again on her face now decided he'd had enough. Nobody, especially Kolya, was going to put his friend through this.

He took out his handgun, walked over to Kolya ignoring the looks of confusion from the rest of his team and placed the barrel of his gun to Kolya's head.

"Tell me you son of a bitch, what is the Genii's interest in Bree?"

He pushed the gun to Kolya's temple so hard he was sure it would leave a bruise.

"It seems you have quite a following my dear."

Aiden pushed the gun harder onto Kolya's temple. Kolya, deciding he had nothing to loose, answered.

"Bree is prophesied, she was destined to be born. She shall rid the Genii of the Wraith. She shall be able to foretell Wraith attacks."

Elizabeth shook her head; she didn't understand what he meant. How Bree could sense the Wraith. She had no Wraith DNA in her unless…

"You have Wraith DNA"

Elizabeth said it in a quiet voice, as if to herself. Kolya simply nodded.

"You haven't guessed my dear? You were with us for months. Every Genii is part Wraith. I know the evil they have done and would love nothing more to destroy them for what they've done, for what they did to my ancestors. And that is why Bree is important."

Elizabeth choked back a sob when she heard his words. When she heard her daughter was part Wraith.  
Kolya wasn't finished.

"It is not by chance we are the parents Elizabeth. It was all pre-determined centuries ago before the Wraith even began their silly genetic quest. It was always going to happen. My ancestors where the first to be experimented on that is why it was always going to be my child, my ancestors at the end where more Wraith then human and you, the reasoning is unknown but you must have power unknown to you. Can you sense when your people are in danger?"

Elizabeth didn't say anything she couldn't. She knew what he was talking about, she'd felt the power he spoke of, she felt when her people were in danger, before she even knew they were. She'd known that John, Rodney and two scientist were in danger on a mission before there was any indication.

Elizabeth looked sharply at Kolya. A look of achievement on his face. She closed her eyes, she couldn't deal with this, didn't want to deal with this. She walked over to him. She grabbed his radio that was laying on the ground.

"Inform your men that they are to allow us safe passage to the Stargate"

When he refused, Aiden dragged Kolya's head back by his hair.

"She won't ask again"

Kolya slowly nodded and Elizabeth held out the radio.

As Kolya informed his men of what had happened and that they were not to harm the Atlantis team, John observed Elizabeth.  
She was broken, fragile, unsure of what to believe or do. He knew all she wanted was to go back and hold her daughter in her arms.  
He saw the limp in her walk, the cut on her lip and the look in Kolya's eyes.  
John, of course, expected the worst. Kolya had done that to her before, it wasn't surprising he'd do it again.

The anger in John began to rise and he tried hard to push it down. Everybody was angry at what had happened. John had never seen Aiden this angry, this viscous. A lot of people loved Elizabeth. A lot of people would give their lives to protect her, John included, but as he watched her he realised, she was there, she was standing strong. She didn't need a protector or a knight in shining armour. She could take care of herself. She was strong after everything she'd been through. She was her own saviour.

TBC…


	13. Chapter 13

Disclaimer: I don't own Stargate Atlantis  
Spoilers: Again, major 'The Gift' spoilers plus everything in season 1  
Note: This is the final chapter (sobs) but I already have a sequel in development (yeah).  
I would like to thank everyone who has reviewed, you've all been so nice and inspiring. Thank you so much.

**ErabuHikari**Thanks, I absolutely adore Aiden. Personally I'm happy Elizabeth showed her strong side, I don't think she'd be one take that situation laying down. She's tough. **  
****Hazeydream**The whole Elizabeth Kolya thing coming through was a something I was unsure about but I put it in anyway. Glad you like the characters all supporting each other.

**

* * *

Atlantis **(Four days later)

Elizabeth sat cross-legged on one of the quieter balconies in the city. Bree was in her arms bouncing happily. Elizabeth just wanted some time alone with her daughter, to watch the beautiful blue water sparkle underneath the deep orange sun.

Elizabeth looked down at Bree.  
As she bounced up and down innocently, it was impossible to imagine what she had inside of her. What she was. Elizabeth knew it wasn't Bree's fault, just like it was Teyla's or the other people who had Wraith DNA inside them. But this felt different. This was her daughter, her own flesh and blood and Elizabeth didn't know how she would deal with this. Kolya and the Genii would always come after Bree, there was no way Bree could be safe in this galaxy.

Since returning to Atlantis four days earlier Elizabeth had done some thinking. Lots of thinking. She could never guarantee her daughters safety but she could try her hardest to protect her daughter.

Elizabeth kissed Bree's temple and sighed. She knew what she had to do.

"Please forgive me Bree. I'm doing this for you"

Tears began to piece Elizabeth's eyes.

(Two days later)

John rolled onto his side to see an empty space. The last few days Elizabeth had been avoiding him and he didn't know why. John sighed, reluctantly got out of bed and walked over to the connecting room. He entered and saw the cradle empty. John sighed, walked out of the room and got a shower. Elizabeth was driving him crazy, she hadn't let him near Bree and she'd been acting lukewarm towards him. John wondered if it had anything to do with Kolya, if he'd done anything to her, John didn't want to even think about what Kolya could have done to her.

John stepped out of the shower, got dried and changed before heading up to the control room.

As he entered the control room and saw Elizabeth in her office with Bree playing in her playpen. He walked past the technicians in the control room and over to Elizabeth's office. He knocked lightly on the door before walking in and going straight over to the playpen, picking up Bree and kissing her lightly and the forehead. While still holding Bree he walked over and sat on the chair facing Elizabeth.

"What's going on with you Elizabeth? You've been lukewarm for days now. Talk to me"

Elizabeth shut her eyes and lifted her head up to face him, she opened and her eyes and sighed.

"Its nothing John, forget about it."

Her eyes drifted back to her laptop and John sighed. Elizabeth was being cold towards him. She had never been cold to him before and he was worried.

"Have I done something wrong Elizabeth? If I have just tell me."

Elizabeth shook her head and turned to him. She couldn't let John go on thinking he'd done something wrong, it wasn't fair and while she wasn't going to tell him until the date grew closer she decided that he had a right to know.  
Elizabeth shut her laptop and sighed.

"John you've done nothing wrong. If anything you've been amazing, that is what makes this so damn hard."

Tears threatened to fall from Elizabeth eyes but she didn't allow them.

"John, I have to keep Bree safe, I'm her mother that's my job"

John nodded. He knew that, he wanted to keep Bree safe too.

"Knowing that the Genii are going to keep coming after Bree is scary to me, John I've made a decision. I wasn't going to tell you until next week, but…but you have a right to know now."

Elizabeth cleared her throat. She knew John's reaction wouldn't be good, she knew everyone else wouldn't like it, but it was necessary.

"John, you know that sometime within the next few weeks we are going to dial Earth with the ZPM found and send copies of the technology we've found"

John nodded, but he was confused about where Elizabeth was going with this.

"John…please don't hate me…I'm going back to Earth and I'm taking Bree."

John sat, silently trying process it, hoping he'd misheard her but the look in her eyes told him that he hadn't. It told him that she was going. John looked down at Bree, he wanted to cry, John Sheppard never cried but the thought of loosing the two people he cared most for, the two people he would die for, it hurt him.

He drew his hand over Bree's brown wispy hair. He didn't want to loose her, John, probably at the beginning the last person on this trip who wanted to be a parent loved this little girl like his own.  
He stayed looking at Bree, he couldn't look at Elizabeth, he couldn't believe she wanted to do this.

Elizabeth sat watching John waiting for him to say something, but he didn't he just kept his eyes firmly on Bree. She knew how much he loved her and that was what hurt the most. She knew John couldn't leave Atlantis, he was too important to the expedition and she knew he wouldn't want to leave the expedition. Elizabeth didn't know how she felt about that, she figured she never would, but there was no time to reflect on that.

"John…John please talk to me, say anything."

John looked at her, eyes blazing.

"How can you even…consider leaving?"

"John, please don't…"

John cut her off and walked out of the room, still holding Bree.

(9 days later) 

Elizabeth stood near the Stargate and embraced Teyla.

"Be safe Dr Weir. Both of you be safe."

Teyla tried to hide the tears forming in her eyes but failed miserably and eventually allowed them to flow freely.

"You too Teyla"

Elizabeth pushed back her own tears and hugged Carson who was standing next to her.

"Good luck lass and remember we're here if you ever decide to come back."

Elizabeth smiled at the Scott and moved over to Rodney.

Rodney had been upset about Elizabeth wanting to leave, if he admitted it he still was. Elizabeth was like a sister to him.  
Elizabeth, knowing that Rodney didn't go in for the whole hugging thing placed her hand on his shoulder.  
She tried hard to find the words but couldn't. She decided light humour was the best way to go.

"Don't go blowing anything else up okay."

Rodney's head snapped up.

"Kavanagh was the one that blew up the machine not…"

Rodney realised what she was doing and smiled.

"I'll miss you too."

Elizabeth moved and tightly hugged Aiden, perhaps the sweetest person she'd ever met.

"Good luck Elizabeth"

Elizabeth nodded still hugging him.

"Thank you for everything Aiden."

She pulled away and smiled at him before looking at the man who'd just entered the room holding Bree.

She knew John was reluctant to let them out of his life but…Atlantis needed a leader and he was the only person with the experience to do it, plus he didn't want to leave.

Handing over Bree would be the most difficult thing John would ever have to do, watching the two people he loved walk through the Stargate would be the most difficult thing to see.  
He walked into the 'Gate room, holding Bree in his arms. He saw Elizabeth hugged Aiden before turning to find John.

She walked the short distance over to him with a sad smile. She kissed on the cheek and she could feel the wetness coming from his eyes. She looked at him with a pleading

"Please don't make this more difficult then it is."

John nodded

"Please reconsider"

Elizabeth shook her head.

"I can't"

John closed his eyes briefly before looking down at Breen and kissing her forehead.

"I love you sweetheart, be good"

He handed Bree to Aiden before grabbing Elizabeth in a long hug.  
John didn't want them to go, but he also knew his two girls would be okay without him. He knew how strong Elizabeth was and he knew she needed to do this alone. As much as he wanted to be with them, he knew that he couldn't. This was Elizabeth's journey in life, her rite of passage and he knew that it was one thing she had to do alone.

He kissed Elizabeth's forehead.

"If anything ever happens get the SGC to dial a wormhole back here. No messing around, no waiting"

Elizabeth nodded

"I will."

She lightly pressed her lips against his and kissed him. She savoured the taste and the feel of it, because she knew she might never feel it again.  
She pulled herself from the hug and John grabbed her hand.

There were three little words he could say now, but that would only make things harder for all of them, instead he opted for something else.

"Keep her safe, keep both of you safe and remember I'm always here and there are always people who care for you and if all the Genii are sadly culled and it's safe again I will send for the two of you."

Elizabeth nodded, she knew the Genii part was a try at humour on his part, but she also knew he meant it.

She pulled her hand from his, barely keeping from breaking down into tears and took Bree from Aiden's hands.  
She looked at the group, the people who she cared dearly about and nodded to John.  
She could do this part but she felt it was important that he did it, so he could let go.

Tears fell from John's eyes, he looked up at the control room and to Peter who was awaiting his word.

"Di…"

He took one last look at Elizabeth and Bree

"Dial up the 'Gate"

Peter nodded and the inner ring of the Stargate began to spin round. Elizabeth kissed John one last time before the event horizon splashed out.  
Elizabeth took that as a sign and calmly entered her IDC.

This was were her journey ended

Fin…

Please keep the flames, rotting fruit and desire to slap me at bay; I ended it this way because the sequel requires a clean slate on which to paint on. The sequel is coming soon.


End file.
